ERS11139244 SAMEA13537274 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737954. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537274 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 24.9512 MAG coverage software Reads (ERR7737954) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561027) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-A-D_J_3_1551__NODE_304_length_45248_cov_14.490735 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585805 sample name Hadza_MoBio_hadza-A-D_J_3_1551__NODE_304_length_45248_cov_14.490735 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738174_virus.898 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139243 SAMEA13537273 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737953. BACPHLIP temperate score 0.09730176211453746 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537273 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 22.3793 MAG coverage software Reads (ERR7737953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_C-REDO_H_7_1595__NODE_939_length_22069_cov_12.971672 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585844 sample name Hadza_MoBio_C-REDO_H_7_1595__NODE_939_length_22069_cov_12.971672 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737953_virus.939 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139264 SAMEA13537294 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737966. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537294 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 15.1672 MAG coverage software Reads (ERR7737966) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 100 Submitter Id Hadza_MoBio_hadza-E-H_P_24_2355__NODE_1133_length_37852_cov_8.884077 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; HMM-based (lower-bound) completeness score 57.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_MoBio_hadza-E-H_P_24_2355__NODE_1133_length_37852_cov_8.884077 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.1150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139241 SAMEA13537271 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737953. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537271 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 7.95469 MAG coverage software Reads (ERR7737953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_C-REDO_H_7_1595__NODE_369_length_42300_cov_4.319541_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585844 sample name Hadza_MoBio_C-REDO_H_7_1595__NODE_369_length_42300_cov_4.319541_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_virus.2288 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139266 SAMEA13537296 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737966. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537296 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 11.4625 MAG coverage software Reads (ERR7737966) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_P_24_2355__NODE_2571_length_19798_cov_6.783429 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_MoBio_hadza-E-H_P_24_2355__NODE_2571_length_19798_cov_6.783429 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737966_virus.2571 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139240 SAMEA13537270 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737623. BACPHLIP temperate score 0.1674559471365639 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537270 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 9.78221 MAG coverage software Reads (ERR7737623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561664) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-I-L_H_8_1236__NODE_97_length_41644_cov_5.562947_1 Viral contig found in MAG ERR7737623_bin.34 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585654 sample name Hadza_MoBio_hadza-I-L_H_8_1236__NODE_97_length_41644_cov_5.562947_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737623_provirus.97 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139239 SAMEA13537269 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737622. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537269 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 27.3072 MAG coverage software Reads (ERR7737622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 416 Submitter Id Hadza_MoBio_hadza-E-H_B_23_1949__NODE_469_length_43030_cov_14.787652 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586088 sample name Hadza_MoBio_hadza-E-H_B_23_1949__NODE_469_length_43030_cov_14.787652 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_virus.1286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139269 SAMEA13537299 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7737967. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537299 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 50.758 MAG coverage software Reads (ERR7737967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559278) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 80 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_C_22_2578__NODE_356_length_51656_cov_29.746719_1 Viral contig found in MAG ERR7737967_bin.11 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586302 sample name Hadza_MoBio_hadza-I-L_C_22_2578__NODE_356_length_51656_cov_29.746719_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738617_provirus.238 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11139238 SAMEA13537268 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7737622. BACPHLIP temperate score 0.06720782038701123 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537268 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 29.1354 MAG coverage software Reads (ERR7737622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_B_23_1949__NODE_1538_length_16195_cov_16.370704 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586088 sample name Hadza_MoBio_hadza-E-H_B_23_1949__NODE_1538_length_16195_cov_16.370704 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.2701 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139272 SAMEA13537302 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737967. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537302 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 17.2645 MAG coverage software Reads (ERR7737967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559278) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 156 Submitter Id Hadza_MoBio_hadza-I-L_C_22_2578__NODE_69_length_104417_cov_10.008166 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8928571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586302 sample name Hadza_MoBio_hadza-I-L_C_22_2578__NODE_69_length_104417_cov_10.008166 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738225_virus.120 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139237 SAMEA13537267 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7737622. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537267 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 37.7324 MAG coverage software Reads (ERR7737622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 111 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_MoBio_hadza-E-H_B_23_1949__NODE_300_length_58150_cov_20.380073_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586088 sample name Hadza_MoBio_hadza-E-H_B_23_1949__NODE_300_length_58150_cov_20.380073_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.832 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139274 SAMEA13537304 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737968. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537304 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 6.49465 MAG coverage software Reads (ERR7737968) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559460) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_O_22_2670__NODE_1040_length_23235_cov_3.561232 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586368 sample name Hadza_MoBio_hadza-I-L_O_22_2670__NODE_1040_length_23235_cov_3.561232 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738265_bin.79 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp900540255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737968_virus.1040 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139233 SAMEA13537263 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737618. BACPHLIP temperate score 0.03912499170499385 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537263 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 33.5583 MAG coverage software Reads (ERR7737618) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560891) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_D_10_1550__NODE_382_length_24986_cov_19.789554 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585804 sample name Hadza_MoBio_C-REDO_D_10_1550__NODE_382_length_24986_cov_19.789554 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_provirus.40 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139234 SAMEA13537264 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737619. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537264 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 15.0678 MAG coverage software Reads (ERR7737619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560055) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 443 Submitter Id Hadza_MoBio_hadza-E-H_B_6_2154__NODE_187_length_46067_cov_7.770385_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586140 sample name Hadza_MoBio_hadza-E-H_B_6_2154__NODE_187_length_46067_cov_7.770385_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745867_provirus.369 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139235 SAMEA13537265 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7737619. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537265 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 7.31249 MAG coverage software Reads (ERR7737619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560055) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_B_6_2154__NODE_2101_length_10339_cov_3.924186 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586140 sample name Hadza_MoBio_hadza-E-H_B_6_2154__NODE_2101_length_10339_cov_3.924186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.29 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900554205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737619_virus.2101 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139253 SAMEA13537283 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737958. BACPHLIP temperate score 0.4125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537283 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 14.8421 MAG coverage software Reads (ERR7737958) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561605) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-A-D_O_20_1212__NODE_270_length_26109_cov_8.107714_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585635 sample name Hadza_MoBio_hadza-A-D_O_20_1212__NODE_270_length_26109_cov_8.107714_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738236_provirus.42 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139254 SAMEA13537284 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7737964. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537284 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 50.1524 MAG coverage software Reads (ERR7737964) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_K_19_1040__NODE_1_length_563034_cov_29.663084_1 Viral contig found in MAG ERR7737964_bin.91 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 70.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585464 sample name Hadza_MoBio_hadza-A-D_K_19_1040__NODE_1_length_563034_cov_29.663084_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745783_provirus.39 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139255 SAMEA13537285 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7737964. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537285 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 17.6682 MAG coverage software Reads (ERR7737964) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 149 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_K_19_1040__NODE_468_length_56279_cov_10.333938_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9629629629629628 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585464 sample name Hadza_MoBio_hadza-A-D_K_19_1040__NODE_468_length_56279_cov_10.333938_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME248826 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_D vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737964_provirus.468 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11139256 SAMEA13537286 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737964. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537286 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 9.35719 MAG coverage software Reads (ERR7737964) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_19_1040__NODE_165_length_103581_cov_5.375599 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 65.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585464 sample name Hadza_MoBio_hadza-A-D_K_19_1040__NODE_165_length_103581_cov_5.375599 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_virus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139258 SAMEA13537288 336724 Myoviridae environmental samples This sample represents an uncultured unclassified Tequatrovirus virus assembled from ERR7737964. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537288 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 574.491 MAG coverage software Reads (ERR7737964) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_19_1040__NODE_72_length_154530_cov_331.296906 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.5648535564853556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585464 sample name Hadza_MoBio_hadza-A-D_K_19_1040__NODE_72_length_154530_cov_331.296906 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0377602 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae; Tequatrovirus; unclassified Tequatrovirus virus enrichment approach none ERS11139260 SAMEA13537290 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737965. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537290 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 14.1974 MAG coverage software Reads (ERR7737965) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561160) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_22_1612__NODE_1113_length_19002_cov_8.814901 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585861 sample name Hadza_MoBio_hadza-A-D_B_22_1612__NODE_1113_length_19002_cov_8.814901 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738552_bin.347 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.6318 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139261 SAMEA13537291 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737965. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537291 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 14.7667 MAG coverage software Reads (ERR7737965) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561160) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_22_1612__NODE_366_length_36390_cov_8.491973 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585861 sample name Hadza_MoBio_hadza-A-D_B_22_1612__NODE_366_length_36390_cov_8.491973 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738241_virus.1176 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139262 SAMEA13537292 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737965. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537292 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 24.4979 MAG coverage software Reads (ERR7737965) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561160) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-A-D_B_22_1612__NODE_84_length_78157_cov_14.728855 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.65625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585861 sample name Hadza_MoBio_hadza-A-D_B_22_1612__NODE_84_length_78157_cov_14.728855 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_virus.77 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139275 SAMEA13537305 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737968. BACPHLIP temperate score 0.03997797356828193 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537305 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 8.12441 MAG coverage software Reads (ERR7737968) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559460) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_O_22_2670__NODE_821_length_32872_cov_4.638634 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586368 sample name Hadza_MoBio_hadza-I-L_O_22_2670__NODE_821_length_32872_cov_4.638634 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738257_virus.590 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139277 SAMEA13537307 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737969. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537307 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 20.9925 MAG coverage software Reads (ERR7737969) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-I-L_D_9_2667__NODE_99_length_160686_cov_12.281547_1 Viral contig found in MAG ERR7737969_bin.176 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6052631578947368 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586365 sample name Hadza_MoBio_hadza-I-L_D_9_2667__NODE_99_length_160686_cov_12.281547_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745577_provirus.301 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139279 SAMEA13537309 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7737969. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537309 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 26.3187 MAG coverage software Reads (ERR7737969) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_D_9_2667__NODE_245_length_103236_cov_15.138766 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 19 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.9178082191780822 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586365 sample name Hadza_MoBio_hadza-I-L_D_9_2667__NODE_245_length_103236_cov_15.138766 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0368853 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139282 SAMEA13537312 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7737970. BACPHLIP temperate score 0.2048458149779736 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537312 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 86.8093 MAG coverage software Reads (ERR7737970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_H_11_1558__NODE_10219_length_5395_cov_51.317789 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585812 sample name Hadza_MoBio_hadza-A-D_H_11_1558__NODE_10219_length_5395_cov_51.317789 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.21679 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11139283 SAMEA13537313 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737970. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537313 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 76.9283 MAG coverage software Reads (ERR7737970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_H_11_1558__NODE_185_length_93506_cov_45.829946 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585812 sample name Hadza_MoBio_hadza-A-D_H_11_1558__NODE_185_length_93506_cov_45.829946 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME280504 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900555735 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738151_provirus.59 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139285 SAMEA13537315 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737970. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537315 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 167.436 MAG coverage software Reads (ERR7737970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 71 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-A-D_H_11_1558__NODE_852_length_38236_cov_99.396001 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585812 sample name Hadza_MoBio_hadza-A-D_H_11_1558__NODE_852_length_38236_cov_99.396001 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_virus.852 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139286 SAMEA13537316 2133760 Siphoviridae environmental samples This sample represents an uncultured Flavobacterium virus Laban provirus assembled from ERR7737971. BACPHLIP temperate score 0.07497530020756127 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537316 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 18.9507 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_277_length_101251_cov_10.981576_1 Viral contig found in MAG ERR7737971_bin.117 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_277_length_101251_cov_10.981576_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_provirus.8 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Labanvirus; Flavobacterium virus Laban virus enrichment approach none ERS11139288 SAMEA13537318 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 virus assembled from ERR7737971. BACPHLIP temperate score 7.8965839962564e-4 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537318 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 20.8991 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_1284_length_37005_cov_11.770635 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_1284_length_37005_cov_11.770635 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738152_bin.166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900546445 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.1061 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11139289 SAMEA13537319 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7737971. BACPHLIP temperate score 0.6902524322062463 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537319 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 73.4451 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 77 Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_1542_length_31927_cov_44.646122 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_1542_length_31927_cov_44.646122 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_virus.119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139294 SAMEA13537324 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7737971. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537324 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 14.358 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 319 Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_774_length_54100_cov_8.337949 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9577464788732394 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_774_length_54100_cov_8.337949 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.2014 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11139296 SAMEA13537326 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737972. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537326 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 36.8937 MAG coverage software Reads (ERR7737972) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560076) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 418 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_B_8_2155__NODE_644_length_58514_cov_20.645670_1 Viral contig found in MAG ERR7737972_bin.164 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586141 sample name Hadza_MoBio_hadza-E-H_B_8_2155__NODE_644_length_58514_cov_20.645670_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737622_virus.559 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139299 SAMEA13537329 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7737972. BACPHLIP temperate score 0.07381662166094104 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537329 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 40.2414 MAG coverage software Reads (ERR7737972) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560076) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-E-H_B_8_2155__NODE_3430_length_15559_cov_22.684601 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586141 sample name Hadza_MoBio_hadza-E-H_B_8_2155__NODE_3430_length_15559_cov_22.684601 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_virus.2406 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139302 SAMEA13537332 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7737973. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537332 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 80.9552 MAG coverage software Reads (ERR7737973) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559436) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 118 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_O_8_2643__NODE_71_length_147858_cov_52.541490_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9705882352941176 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586347 sample name Hadza_MoBio_hadza-I-L_O_8_2643__NODE_71_length_147858_cov_52.541490_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738531_virus.150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139245 SAMEA13537275 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7737954. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537275 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 18.7772 MAG coverage software Reads (ERR7737954) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561027) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_J_3_1551__NODE_57_length_106893_cov_10.370019 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.954954954954955 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585805 sample name Hadza_MoBio_hadza-A-D_J_3_1551__NODE_57_length_106893_cov_10.370019 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_virus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11139247 SAMEA13537277 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737955. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537277 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 15.4261 MAG coverage software Reads (ERR7737955) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560488) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 173 Submitter Id Hadza_MoBio_F_H_7_1932__NODE_46_length_124083_cov_8.303598_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586073 sample name Hadza_MoBio_F_H_7_1932__NODE_46_length_124083_cov_8.303598_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.2062 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139248 SAMEA13537278 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737955. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537278 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 450.565 MAG coverage software Reads (ERR7737955) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560488) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_F_H_7_1932__NODE_447_length_32519_cov_251.256766 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586073 sample name Hadza_MoBio_F_H_7_1932__NODE_447_length_32519_cov_251.256766 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095938 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745876_virus.275 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139249 SAMEA13537279 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737956. BACPHLIP temperate score 0.01486784140969163 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537279 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 73.6464 MAG coverage software Reads (ERR7737956) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561101) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_C-REDO_H_8_1596__NODE_247_length_67800_cov_44.854865_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585845 sample name Hadza_MoBio_C-REDO_H_8_1596__NODE_247_length_67800_cov_44.854865_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.2294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139250 SAMEA13537280 1701671 uncultured podovirus This sample represents an uncultured CrAss-like virus sp. virus assembled from ERR7737956. BACPHLIP temperate score 0.13997797356828195 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537280 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 25.9982 MAG coverage software Reads (ERR7737956) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561101) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_C-REDO_H_8_1596__NODE_140_length_96359_cov_15.273052 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585845 sample name Hadza_MoBio_C-REDO_H_8_1596__NODE_140_length_96359_cov_15.273052 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746465_bin.138 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA3388;s__UBA3388 sp900546465 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738149_virus.130 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; CrAss-like virus sp. virus enrichment approach none ERS11139251 SAMEA13537281 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737956. BACPHLIP temperate score 0.1875187332894936 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537281 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:37Z INSDC last update 2022-12-26T20:28:37Z INSDC status public MAG coverage depth 7.89504 MAG coverage software Reads (ERR7737956) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561101) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_C-REDO_H_8_1596__NODE_4295_length_7953_cov_4.598019 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585845 sample name Hadza_MoBio_C-REDO_H_8_1596__NODE_4295_length_7953_cov_4.598019 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus vestibularis;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737956_virus.4295 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139252 SAMEA13537282 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737956. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537282 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 13.2611 MAG coverage software Reads (ERR7737956) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561101) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_H_8_1596__NODE_637_length_35923_cov_7.802963 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585845 sample name Hadza_MoBio_C-REDO_H_8_1596__NODE_637_length_35923_cov_7.802963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737956_virus.637 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139263 SAMEA13537293 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737966. BACPHLIP temperate score 0.23526345696647236 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537293 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 15.5973 MAG coverage software Reads (ERR7737966) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_P_24_2355__NODE_504_length_62311_cov_8.799370_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_MoBio_hadza-E-H_P_24_2355__NODE_504_length_62311_cov_8.799370_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_provirus.514 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139265 SAMEA13537295 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737966. BACPHLIP temperate score 0.15566732807002084 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537295 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 35.1554 MAG coverage software Reads (ERR7737966) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-E-H_P_24_2355__NODE_1496_length_31066_cov_21.912388 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_MoBio_hadza-E-H_P_24_2355__NODE_1496_length_31066_cov_21.912388 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738568_bin.12 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552965 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.2368 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139267 SAMEA13537297 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737966. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537297 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 23.4571 MAG coverage software Reads (ERR7737966) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_P_24_2355__NODE_613_length_55760_cov_13.336458 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_MoBio_hadza-E-H_P_24_2355__NODE_613_length_55760_cov_13.336458 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_virus.1003 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139268 SAMEA13537298 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7737966. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537298 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 40.5787 MAG coverage software Reads (ERR7737966) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 96 Submitter Id Hadza_MoBio_hadza-E-H_P_24_2355__NODE_909_length_44575_cov_23.228370 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_MoBio_hadza-E-H_P_24_2355__NODE_909_length_44575_cov_23.228370 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738568_bin.12 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552965 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_provirus.80 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11139270 SAMEA13537300 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7737967. BACPHLIP temperate score 0.04793421803331155 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537300 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 160.373 MAG coverage software Reads (ERR7737967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559278) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_C_22_2578__NODE_16_length_181530_cov_92.136498 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586302 sample name Hadza_MoBio_hadza-I-L_C_22_2578__NODE_16_length_181530_cov_92.136498 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.144 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139273 SAMEA13537303 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737968. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537303 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 18.2144 MAG coverage software Reads (ERR7737968) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559460) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_O_22_2670__NODE_335_length_82601_cov_11.628241_1 Viral contig found in MAG ERR7737968_bin.54 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586368 sample name Hadza_MoBio_hadza-I-L_O_22_2670__NODE_335_length_82601_cov_11.628241_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738171_provirus.78 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139276 SAMEA13537306 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7737969. BACPHLIP temperate score 0.05270140052539582 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537306 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 135.631 MAG coverage software Reads (ERR7737969) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_D_9_2667__NODE_580_length_61854_cov_79.565987_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586365 sample name Hadza_MoBio_hadza-I-L_D_9_2667__NODE_580_length_61854_cov_79.565987_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139280 SAMEA13537310 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737969. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537310 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 159.174 MAG coverage software Reads (ERR7737969) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-I-L_D_9_2667__NODE_633_length_58755_cov_94.651062 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; HMM-based (lower-bound) completeness score 68.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586365 sample name Hadza_MoBio_hadza-I-L_D_9_2667__NODE_633_length_58755_cov_94.651062 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737969_virus.633 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139284 SAMEA13537314 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737970. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537314 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 31.3994 MAG coverage software Reads (ERR7737970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_H_11_1558__NODE_35_length_186723_cov_18.207076 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 17 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.7380952380952381 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585812 sample name Hadza_MoBio_hadza-A-D_H_11_1558__NODE_35_length_186723_cov_18.207076 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.166 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139291 SAMEA13537321 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737971. BACPHLIP temperate score 0.00991189427312775 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537321 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 14.7666 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_2955_length_17200_cov_8.545816 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_2955_length_17200_cov_8.545816 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.3045 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139292 SAMEA13537322 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7737971. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537322 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 13.7284 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_3867_length_13166_cov_7.972343 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_3867_length_13166_cov_7.972343 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.12313 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11139295 SAMEA13537325 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7737972. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537325 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 46.094 MAG coverage software Reads (ERR7737972) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560076) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 228 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_B_8_2155__NODE_214_length_118782_cov_28.183649_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.926829268292683 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586141 sample name Hadza_MoBio_hadza-E-H_B_8_2155__NODE_214_length_118782_cov_28.183649_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_provirus.208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139297 SAMEA13537327 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737972. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537327 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 32.6961 MAG coverage software Reads (ERR7737972) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560076) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_B_8_2155__NODE_1202_length_36074_cov_18.365114 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586141 sample name Hadza_MoBio_hadza-E-H_B_8_2155__NODE_1202_length_36074_cov_18.365114 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738209_virus.1870 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139298 SAMEA13537328 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737972. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537328 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 10.4505 MAG coverage software Reads (ERR7737972) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560076) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_B_8_2155__NODE_2108_length_23178_cov_5.886022 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586141 sample name Hadza_MoBio_hadza-E-H_B_8_2155__NODE_2108_length_23178_cov_5.886022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_virus.436 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139305 SAMEA13537335 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737973. BACPHLIP temperate score 0.02597739359623315 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537335 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 30.5114 MAG coverage software Reads (ERR7737973) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559436) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_O_8_2643__NODE_2717_length_17895_cov_18.176002 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586347 sample name Hadza_MoBio_hadza-I-L_O_8_2643__NODE_2717_length_17895_cov_18.176002 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.3678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139307 SAMEA13537337 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7737973. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537337 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 14.9572 MAG coverage software Reads (ERR7737973) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559436) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 172 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_O_8_2643__NODE_863_length_42303_cov_8.581182 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; HMM-based (lower-bound) completeness score 81.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586347 sample name Hadza_MoBio_hadza-I-L_O_8_2643__NODE_863_length_42303_cov_8.581182 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139311 SAMEA13537341 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737974. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537341 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 26.4195 MAG coverage software Reads (ERR7737974) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560365) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_M_17_1798__NODE_429_length_52332_cov_15.309789 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-18 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.35 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586007 sample name Hadza_MoBio_hadza-E-H_M_17_1798__NODE_429_length_52332_cov_15.309789 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_virus.697 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139315 SAMEA13537345 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738141. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537345 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 53.702 MAG coverage software Reads (ERR7738141) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559284) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 71 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-I-L_O_21_2512__NODE_71_length_138888_cov_32.205193_1 Viral contig found in MAG ERR7738141_bin.7 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 86.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586285 sample name Hadza_MoBio_hadza-I-L_O_21_2512__NODE_71_length_138888_cov_32.205193_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746741_bin.80 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;s__RUG572 sp900547945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738141_provirus.71 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139318 SAMEA13537348 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738141. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537348 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 77.6957 MAG coverage software Reads (ERR7738141) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559284) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-I-L_O_21_2512__NODE_864_length_39422_cov_43.407345 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586285 sample name Hadza_MoBio_hadza-I-L_O_21_2512__NODE_864_length_39422_cov_43.407345 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.780 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139319 SAMEA13537349 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738142. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537349 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 17.2684 MAG coverage software Reads (ERR7738142) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559809) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-I-L_G_23_2446__NODE_29_length_173332_cov_9.830562_1 Viral contig found in MAG ERR7738142_bin.70 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586240 sample name Hadza_MoBio_hadza-I-L_G_23_2446__NODE_29_length_173332_cov_9.830562_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738142_provirus.29 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139321 SAMEA13537351 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738142. BACPHLIP temperate score 0.7924559471365639 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537351 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 20.8254 MAG coverage software Reads (ERR7738142) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559809) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 173 Submitter Id Hadza_MoBio_hadza-I-L_G_23_2446__NODE_364_length_62345_cov_12.057172 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586240 sample name Hadza_MoBio_hadza-I-L_G_23_2446__NODE_364_length_62345_cov_12.057172 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745371_virus.359 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139322 SAMEA13537352 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738142. BACPHLIP temperate score 0.9299559471365638 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537352 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 74.6221 MAG coverage software Reads (ERR7738142) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559809) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_G_23_2446__NODE_732_length_42602_cov_42.164821 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586240 sample name Hadza_MoBio_hadza-I-L_G_23_2446__NODE_732_length_42602_cov_42.164821 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018425 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__CAG-791 sp000431495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738614_provirus.14 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139325 SAMEA13537355 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738143. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537355 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 10.0132 MAG coverage software Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_MoBio_hadza-I-L_K_3_2480__NODE_882_length_53881_cov_5.454910_1 Viral contig found in MAG ERR7738143_bin.134 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586254 sample name Hadza_MoBio_hadza-I-L_K_3_2480__NODE_882_length_53881_cov_5.454910_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738143_provirus.882 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139328 SAMEA13537358 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738143. BACPHLIP temperate score 0.06434525602217449 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537358 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 14.4815 MAG coverage software Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_K_3_2480__NODE_4337_length_13253_cov_8.264966 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586254 sample name Hadza_MoBio_hadza-I-L_K_3_2480__NODE_4337_length_13253_cov_8.264966 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_virus.9015 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139329 SAMEA13537359 340016 uncultured virus This sample represents an uncultured Methanobacterium virus PhiF1 virus assembled from ERR7738143. BACPHLIP temperate score 0.45535389006526233 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537359 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 22.7061 MAG coverage software Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 509 Submitter Id Hadza_MoBio_hadza-I-L_K_3_2480__NODE_876_length_53981_cov_13.039088 Viral contig found in MAG ERR7738143_bin.85 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586254 sample name Hadza_MoBio_hadza-I-L_K_3_2480__NODE_876_length_53981_cov_13.039088 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746779_virus.285 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Methanobacterium virus PhiF1 virus enrichment approach none ERS11139334 SAMEA13537364 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738145. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537364 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 143.079 MAG coverage software Reads (ERR7738145) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559588) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_J_24_2316__NODE_416_length_70568_cov_87.007022 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586188 sample name Hadza_MoBio_hadza-E-H_J_24_2316__NODE_416_length_70568_cov_87.007022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738155_virus.49 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139336 SAMEA13537366 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738146. BACPHLIP temperate score 0.04430120315873834 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537366 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 11.9659 MAG coverage software Reads (ERR7738146) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-I-L_M_24_2678__NODE_1465_length_26456_cov_6.978506_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586376 sample name Hadza_MoBio_hadza-I-L_M_24_2678__NODE_1465_length_26456_cov_6.978506_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME165031 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__Collinsella sp900542825 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_virus.1159 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139337 SAMEA13537367 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738146. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537367 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 166.681 MAG coverage software Reads (ERR7738146) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 114 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-I-L_M_24_2678__NODE_768_length_42998_cov_99.602665_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586376 sample name Hadza_MoBio_hadza-I-L_M_24_2678__NODE_768_length_42998_cov_99.602665_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737966_provirus.195 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139340 SAMEA13537370 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7738146. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537370 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 44.3163 MAG coverage software Reads (ERR7738146) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_M_24_2678__NODE_789_length_42223_cov_26.320647 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586376 sample name Hadza_MoBio_hadza-I-L_M_24_2678__NODE_789_length_42223_cov_26.320647 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738192_bin.234 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp900543455 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745388_virus.1037 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11139346 SAMEA13537376 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738148. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537376 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 13.3235 MAG coverage software Reads (ERR7738148) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559582) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 94 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_J_18_2314__NODE_9_length_346542_cov_7.864214_1 Viral contig found in MAG ERR7738148_bin.20 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586186 sample name Hadza_MoBio_hadza-E-H_J_18_2314__NODE_9_length_346542_cov_7.864214_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738148_bin.20 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A;s__Selenomonas_A sp900769615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738145_provirus.21 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139347 SAMEA13537377 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738148. BACPHLIP temperate score 0.02747797356828193 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537377 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 7.97291 MAG coverage software Reads (ERR7738148) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559582) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_J_18_2314__NODE_2040_length_16981_cov_4.476514 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586186 sample name Hadza_MoBio_hadza-E-H_J_18_2314__NODE_2040_length_16981_cov_4.476514 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.2701 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139349 SAMEA13537379 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738149. BACPHLIP temperate score 0.01486784140969163 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537379 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 91.9772 MAG coverage software Reads (ERR7738149) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561419) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_C-REDO_A_10_1510__NODE_232_length_67800_cov_55.375323_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585766 sample name Hadza_MoBio_C-REDO_A_10_1510__NODE_232_length_67800_cov_55.375323_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.2294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139350 SAMEA13537380 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738149. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537380 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 17.3301 MAG coverage software Reads (ERR7738149) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561419) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_C-REDO_A_10_1510__NODE_119_length_100792_cov_10.038554 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.9012345679012346 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585766 sample name Hadza_MoBio_C-REDO_A_10_1510__NODE_119_length_100792_cov_10.038554 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737956_virus.124 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139351 SAMEA13537381 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738149. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537381 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 43.7964 MAG coverage software Reads (ERR7738149) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561419) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 102 Submitter Id Hadza_MoBio_C-REDO_A_10_1510__NODE_334_length_53845_cov_25.938328 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585766 sample name Hadza_MoBio_C-REDO_A_10_1510__NODE_334_length_53845_cov_25.938328 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139353 SAMEA13537383 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738149. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537383 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 35.6031 MAG coverage software Reads (ERR7738149) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561419) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_C-REDO_A_10_1510__NODE_75_length_125971_cov_20.819014 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 30 number of unique standard tRNAs extracted 20 percent of BLAST hits supporting viral taxonomy 0.676923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585766 sample name Hadza_MoBio_C-REDO_A_10_1510__NODE_75_length_125971_cov_20.819014 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME246739 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;s__Lachnospira eligens_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738149_virus.75 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11139354 SAMEA13537384 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738150. BACPHLIP temperate score 0.04245594713656388 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537384 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 17.999 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_293_length_103270_cov_10.424845_1 Viral contig found in MAG ERR7738150_bin.229 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_293_length_103270_cov_10.424845_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738179_virus.1416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139355 SAMEA13537385 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738150. BACPHLIP temperate score 0.09997166296723237 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537385 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 23.3784 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_690_length_60830_cov_13.157260_1 Viral contig found in MAG ERR7738150_bin.153 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_690_length_60830_cov_13.157260_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME258969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__CAG-269 sp001916005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.2731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139357 SAMEA13537387 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738150. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537387 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 19.2391 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2421 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_1368_length_37680_cov_11.286440 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_1368_length_37680_cov_11.286440 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0281755 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139358 SAMEA13537388 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738150. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537388 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 11.6389 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_1782_length_30873_cov_6.761690 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_1782_length_30873_cov_6.761690 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1159 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139359 SAMEA13537389 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738150. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537389 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 1505.28 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_283_length_104622_cov_836.446860 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_283_length_104622_cov_836.446860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745429_virus.160 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11139361 SAMEA13537391 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738150. BACPHLIP temperate score 0.6375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537391 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 10.7826 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_769_length_56097_cov_6.318815 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6486486486486487 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_769_length_56097_cov_6.318815 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.1297 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139301 SAMEA13537331 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737973. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537331 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 321.785 MAG coverage software Reads (ERR7737973) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559436) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-I-L_O_8_2643__NODE_167_length_103647_cov_199.156155_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586347 sample name Hadza_MoBio_hadza-I-L_O_8_2643__NODE_167_length_103647_cov_199.156155_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139303 SAMEA13537333 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737973. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537333 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 19.5325 MAG coverage software Reads (ERR7737973) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559436) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_O_8_2643__NODE_1528_length_28899_cov_11.400285 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586347 sample name Hadza_MoBio_hadza-I-L_O_8_2643__NODE_1528_length_28899_cov_11.400285 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139304 SAMEA13537334 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737973. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537334 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 6.34627 MAG coverage software Reads (ERR7737973) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559436) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 112 Submitter Id Hadza_MoBio_hadza-I-L_O_8_2643__NODE_1795_length_25405_cov_3.473823 Viral contig found in MAG ERR7737973_bin.144 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586347 sample name Hadza_MoBio_hadza-I-L_O_8_2643__NODE_1795_length_25405_cov_3.473823 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139306 SAMEA13537336 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737973. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537336 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 16.9934 MAG coverage software Reads (ERR7737973) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559436) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-I-L_O_8_2643__NODE_507_length_59081_cov_9.683208 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586347 sample name Hadza_MoBio_hadza-I-L_O_8_2643__NODE_507_length_59081_cov_9.683208 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_provirus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139309 SAMEA13537339 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737974. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537339 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 14.3761 MAG coverage software Reads (ERR7737974) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560365) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_M_17_1798__NODE_1102_length_29421_cov_7.868627 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-18 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586007 sample name Hadza_MoBio_hadza-E-H_M_17_1798__NODE_1102_length_29421_cov_7.868627 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_virus.731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139310 SAMEA13537340 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737974. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537340 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 43.1343 MAG coverage software Reads (ERR7737974) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560365) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 82 Submitter Id Hadza_MoBio_hadza-E-H_M_17_1798__NODE_234_length_73223_cov_25.161950 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-18 completeness approach CheckV; HMM-based (lower-bound) completeness score 79.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.34285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586007 sample name Hadza_MoBio_hadza-E-H_M_17_1798__NODE_234_length_73223_cov_25.161950 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_virus.251 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139312 SAMEA13537342 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7737974. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537342 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 6.28116 MAG coverage software Reads (ERR7737974) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560365) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_M_17_1798__NODE_6741_length_8800_cov_3.383125 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-18 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586007 sample name Hadza_MoBio_hadza-E-H_M_17_1798__NODE_6741_length_8800_cov_3.383125 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_provirus.3519 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11139314 SAMEA13537344 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738141. BACPHLIP temperate score 0.23584667126223852 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537344 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 39.1946 MAG coverage software Reads (ERR7738141) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559284) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_O_21_2512__NODE_22_length_251009_cov_23.456462_1 Viral contig found in MAG ERR7738141_bin.63 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586285 sample name Hadza_MoBio_hadza-I-L_O_21_2512__NODE_22_length_251009_cov_23.456462_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_provirus.75 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139316 SAMEA13537346 2133760 Siphoviridae environmental samples This sample represents an uncultured Cellulophaga phage Ingeline_8 virus assembled from ERR7738141. BACPHLIP temperate score 0.01734581497797357 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537346 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 9.20618 MAG coverage software Reads (ERR7738141) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559284) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-I-L_O_21_2512__NODE_1378_length_28198_cov_4.703567 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586285 sample name Hadza_MoBio_hadza-I-L_O_21_2512__NODE_1378_length_28198_cov_4.703567 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cellulophaga phage Ingeline_8 virus enrichment approach none ERS11139317 SAMEA13537347 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738141. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537347 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 82.1006 MAG coverage software Reads (ERR7738141) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559284) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 113 Submitter Id Hadza_MoBio_hadza-I-L_O_21_2512__NODE_264_length_77571_cov_54.291532 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586285 sample name Hadza_MoBio_hadza-I-L_O_21_2512__NODE_264_length_77571_cov_54.291532 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738141_virus.264 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11139320 SAMEA13537350 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738142. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537350 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 28.5503 MAG coverage software Reads (ERR7738142) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559809) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-I-L_G_23_2446__NODE_1053_length_33067_cov_16.565050 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586240 sample name Hadza_MoBio_hadza-I-L_G_23_2446__NODE_1053_length_33067_cov_16.565050 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.1267 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139323 SAMEA13537353 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738143. BACPHLIP temperate score 0.11497797356828196 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537353 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 16.3461 MAG coverage software Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-I-L_K_3_2480__NODE_183_length_131500_cov_9.317494_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586254 sample name Hadza_MoBio_hadza-I-L_K_3_2480__NODE_183_length_131500_cov_9.317494_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139324 SAMEA13537354 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738143. BACPHLIP temperate score 0.11216960352422913 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537354 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 10.5034 MAG coverage software Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 392 Submitter Id Hadza_MoBio_hadza-I-L_K_3_2480__NODE_544_length_72809_cov_5.926374_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586254 sample name Hadza_MoBio_hadza-I-L_K_3_2480__NODE_544_length_72809_cov_5.926374_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_provirus.1616 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139363 SAMEA13537393 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738151. BACPHLIP temperate score 0.04245594713656388 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537393 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 17.8678 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_296_length_104393_cov_11.022892_1 Viral contig found in MAG ERR7738151_bin.118 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_296_length_104393_cov_11.022892_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738179_virus.1416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139365 SAMEA13537395 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738151. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537395 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 24.7672 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_1175_length_41921_cov_14.458752 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_1175_length_41921_cov_14.458752 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UMGS1585;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.3089 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139366 SAMEA13537396 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738151. BACPHLIP temperate score 0.04790239424235011 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537396 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 13.9988 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_15671_length_5313_cov_9.050802 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_15671_length_5313_cov_9.050802 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738552_bin.347 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.30465 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11139367 SAMEA13537397 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738151. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537397 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 186.731 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_2202_length_25881_cov_115.773330 Viral contig found in MAG ERR7738151_bin.199 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_2202_length_25881_cov_115.773330 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_provirus.37 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139368 SAMEA13537398 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738151. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537398 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 49.2912 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_40983_length_2550_cov_30.147594 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_40983_length_2550_cov_30.147594 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.13523 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11139369 SAMEA13537399 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738151. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537399 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 11.6395 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_765_length_57309_cov_6.798120 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.4230769230769231 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_765_length_57309_cov_6.798120 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738151_virus.765 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139372 SAMEA13537402 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738152. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537402 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 25.7077 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 113 Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_1057_length_36083_cov_14.851164 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_1057_length_36083_cov_14.851164 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.1518 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139373 SAMEA13537403 340016 uncultured virus This sample represents an uncultured Poxviridae virus assembled from ERR7738152. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537403 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 88.0902 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_141_length_133713_cov_50.655467 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_141_length_133713_cov_50.655467 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_virus.141 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota; Pokkesviricetes; Chitovirales; Poxviridae virus enrichment approach none ERS11139374 SAMEA13537404 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738152. BACPHLIP temperate score 0.08589947736157162 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537404 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 26.875 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_2247_length_20034_cov_16.845768 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_2247_length_20034_cov_16.845768 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_virus.395 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139376 SAMEA13537406 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738152. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537406 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 23.61 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_554_length_54997_cov_14.069446 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_554_length_54997_cov_14.069446 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME158868 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900549635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.2017 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139377 SAMEA13537407 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738152. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537407 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 16.2893 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_754_length_45436_cov_9.234397 Viral contig found in MAG ERR7738152_bin.164 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_754_length_45436_cov_9.234397 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.950 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139379 SAMEA13537409 2133760 Siphoviridae environmental samples This sample represents an uncultured unclassified Lambdavirus provirus assembled from ERR7738153. BACPHLIP temperate score 0.11321451267193008 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537409 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 142.503 MAG coverage software Reads (ERR7738153) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559832) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3747 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_K_17_2487__NODE_208_length_76991_cov_85.522766_1 Viral contig found in MAG ERR7738153_bin.19 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5652173913043478 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586261 sample name Hadza_MoBio_hadza-I-L_K_17_2487__NODE_208_length_76991_cov_85.522766_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0300980 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus; unclassified Lambdavirus virus enrichment approach none ERS11139381 SAMEA13537411 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae provirus assembled from ERR7738154. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537411 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 26.8363 MAG coverage software Reads (ERR7738154) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561215) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-A-D_B_1_1600__NODE_18_length_166231_cov_15.689577_1 Viral contig found in MAG ERR7738154_bin.60 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585849 sample name Hadza_MoBio_hadza-A-D_B_1_1600__NODE_18_length_166231_cov_15.689577_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.1478 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11139384 SAMEA13537414 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738155. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537414 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 33.8472 MAG coverage software Reads (ERR7738155) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560511) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_B_1_1938__NODE_175_length_90103_cov_19.747484_1 Viral contig found in MAG ERR7738155_bin.37 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9655172413793104 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586078 sample name Hadza_MoBio_hadza-E-H_B_1_1938__NODE_175_length_90103_cov_19.747484_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125893 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger formicilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0337868 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139385 SAMEA13537415 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738155. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537415 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 8.48729 MAG coverage software Reads (ERR7738155) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560511) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_B_1_1938__NODE_1147_length_22016_cov_4.599617 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586078 sample name Hadza_MoBio_hadza-E-H_B_1_1938__NODE_1147_length_22016_cov_4.599617 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738155_bin.62 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__Megasphaera sp002431345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_provirus.21 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139386 SAMEA13537416 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738155. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537416 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 9.83597 MAG coverage software Reads (ERR7738155) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560511) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 555 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_B_1_1938__NODE_577_length_39778_cov_5.498275 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586078 sample name Hadza_MoBio_hadza-E-H_B_1_1938__NODE_577_length_39778_cov_5.498275 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0369830 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139387 SAMEA13537417 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738155. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537417 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 42.238 MAG coverage software Reads (ERR7738155) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560511) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-E-H_B_1_1938__NODE_792_length_30886_cov_24.003765 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586078 sample name Hadza_MoBio_hadza-E-H_B_1_1938__NODE_792_length_30886_cov_24.003765 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738237_provirus.710 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139388 SAMEA13537418 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738156. BACPHLIP temperate score 0.839977973568282 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537418 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 149.84 MAG coverage software Reads (ERR7738156) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559605) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 98 Submitter Id Hadza_MoBio_hadza-E-H_J_10_2310__NODE_223_length_80159_cov_95.324580_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586182 sample name Hadza_MoBio_hadza-E-H_J_10_2310__NODE_223_length_80159_cov_95.324580_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.895 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139390 SAMEA13537420 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738156. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537420 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 11.559 MAG coverage software Reads (ERR7738156) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559605) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1527 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_hadza-E-H_J_10_2310__NODE_372_length_63199_cov_6.960267 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586182 sample name Hadza_MoBio_hadza-E-H_J_10_2310__NODE_372_length_63199_cov_6.960267 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738156_virus.372 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11139391 SAMEA13537421 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738156. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537421 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 11.129 MAG coverage software Reads (ERR7738156) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559605) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 346 Number of CRISPR spacer hits supporting host taxonomy 775 Submitter Id Hadza_MoBio_hadza-E-H_J_10_2310__NODE_662_length_45098_cov_6.209058 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586182 sample name Hadza_MoBio_hadza-E-H_J_10_2310__NODE_662_length_45098_cov_6.209058 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.561 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139393 SAMEA13537423 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738157. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537423 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 31.3901 MAG coverage software Reads (ERR7738157) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-I-L_D_19_2669__NODE_438_length_74695_cov_18.419470_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6129032258064516 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586367 sample name Hadza_MoBio_hadza-I-L_D_19_2669__NODE_438_length_74695_cov_18.419470_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745577_provirus.301 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139394 SAMEA13537424 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lugh provirus assembled from ERR7738157. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537424 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 26.737 MAG coverage software Reads (ERR7738157) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Hadza_MoBio_hadza-I-L_D_19_2669__NODE_808_length_50338_cov_15.875768_1 Viral contig found in MAG ERR7738157_bin.81 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586367 sample name Hadza_MoBio_hadza-I-L_D_19_2669__NODE_808_length_50338_cov_15.875768_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745427_virus.461 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lughvirus; Faecalibacterium virus Lugh virus enrichment approach none ERS11139395 SAMEA13537425 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738157. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537425 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 25.6069 MAG coverage software Reads (ERR7738157) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 67 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_hadza-I-L_D_19_2669__NODE_1299_length_36429_cov_15.104203 Viral contig found in MAG ERR7738157_bin.126 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586367 sample name Hadza_MoBio_hadza-I-L_D_19_2669__NODE_1299_length_36429_cov_15.104203 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737974_provirus.29 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139396 SAMEA13537426 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738157. BACPHLIP temperate score 0.05501014145734777 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537426 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 7.13712 MAG coverage software Reads (ERR7738157) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_D_19_2669__NODE_2210_length_23159_cov_4.074647 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586367 sample name Hadza_MoBio_hadza-I-L_D_19_2669__NODE_2210_length_23159_cov_4.074647 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014720 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UMGS1585;s__UMGS1585 sp900553205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.3089 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139397 SAMEA13537427 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738157. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537427 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 124.804 MAG coverage software Reads (ERR7738157) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 243 Submitter Id Hadza_MoBio_hadza-I-L_D_19_2669__NODE_585_length_62483_cov_72.556405 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586367 sample name Hadza_MoBio_hadza-I-L_D_19_2669__NODE_585_length_62483_cov_72.556405 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738182_virus.387 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139398 SAMEA13537428 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus provirus assembled from ERR7738158. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537428 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 10.8556 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_1139_length_44303_cov_5.889522_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_1139_length_44303_cov_5.889522_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_provirus.1139 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11139402 SAMEA13537432 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738158. BACPHLIP temperate score 0.07665282975512436 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537432 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 8.94045 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_1517_length_36756_cov_5.086207 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_1517_length_36756_cov_5.086207 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738251_virus.875 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139404 SAMEA13537434 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738158. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537434 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 22.2901 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_587_length_65261_cov_13.029562 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_587_length_65261_cov_13.029562 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738604_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432655 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745329_virus.181 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139406 SAMEA13537436 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7738159. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537436 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 51.1795 MAG coverage software Reads (ERR7738159) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559470) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-I-L_O_24_2672__NODE_4_length_481924_cov_29.869463_1 Viral contig found in MAG ERR7738159_bin.29 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586370 sample name Hadza_MoBio_hadza-I-L_O_24_2672__NODE_4_length_481924_cov_29.869463_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737968_provirus.2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11139407 SAMEA13537437 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738159. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537437 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 15.0178 MAG coverage software Reads (ERR7738159) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559470) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_hadza-I-L_O_24_2672__NODE_280_length_86031_cov_8.738407 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; HMM-based (lower-bound) completeness score 59.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4583333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586370 sample name Hadza_MoBio_hadza-I-L_O_24_2672__NODE_280_length_86031_cov_8.738407 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738201_virus.326 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139408 SAMEA13537438 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738160. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537438 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 37.0583 MAG coverage software Reads (ERR7738160) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559708) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_P_2_2343__NODE_1360_length_34637_cov_20.761198_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586213 sample name Hadza_MoBio_hadza-E-H_P_2_2343__NODE_1360_length_34637_cov_20.761198_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_provirus.2857 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139409 SAMEA13537439 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738160. BACPHLIP temperate score 0.2702991463254911 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537439 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 12.0173 MAG coverage software Reads (ERR7738160) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559708) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-E-H_P_2_2343__NODE_452_length_68009_cov_6.557661_1 Viral contig found in MAG ERR7738160_bin.24 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586213 sample name Hadza_MoBio_hadza-E-H_P_2_2343__NODE_452_length_68009_cov_6.557661_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738160_provirus.452 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139410 SAMEA13537440 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738160. BACPHLIP temperate score 0.05270140052539582 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537440 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 164.061 MAG coverage software Reads (ERR7738160) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559708) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_2_2343__NODE_880_length_45836_cov_93.558579_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586213 sample name Hadza_MoBio_hadza-E-H_P_2_2343__NODE_880_length_45836_cov_93.558579_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139411 SAMEA13537441 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738160. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537441 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 7.2012 MAG coverage software Reads (ERR7738160) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559708) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_P_2_2343__NODE_1839_length_27053_cov_3.950030 Viral contig found in MAG ERR7738160_bin.7 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586213 sample name Hadza_MoBio_hadza-E-H_P_2_2343__NODE_1839_length_27053_cov_3.950030 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738160_virus.1839 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139236 SAMEA13537266 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737621. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537266 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 1422.97 MAG coverage software Reads (ERR7737621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560434) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 116 Number of CRISPR spacer hits supporting host taxonomy 435 Submitter Id Hadza_MoBio_hadza-E-H_E_16_1853__NODE_1_length_681967_cov_842.858445_1 Viral contig found in MAG ERR7737621_bin.3 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586038 sample name Hadza_MoBio_hadza-E-H_E_16_1853__NODE_1_length_681967_cov_842.858445_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095938 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737621_provirus.1 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139242 SAMEA13537272 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737953. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537272 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 19.985 MAG coverage software Reads (ERR7737953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 204 Submitter Id Hadza_MoBio_C-REDO_H_7_1595__NODE_234_length_55319_cov_11.454763 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585844 sample name Hadza_MoBio_C-REDO_H_7_1595__NODE_234_length_55319_cov_11.454763 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737953_virus.234 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139257 SAMEA13537287 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737964. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537287 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 27.467 MAG coverage software Reads (ERR7737964) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_K_19_1040__NODE_32_length_210607_cov_15.926334 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.5576923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585464 sample name Hadza_MoBio_hadza-A-D_K_19_1040__NODE_32_length_210607_cov_15.926334 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737964_virus.32 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139259 SAMEA13537289 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737964. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537289 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 41.4412 MAG coverage software Reads (ERR7737964) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 77 Submitter Id Hadza_MoBio_hadza-A-D_K_19_1040__NODE_891_length_37856_cov_24.415892 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9032258064516128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585464 sample name Hadza_MoBio_hadza-A-D_K_19_1040__NODE_891_length_37856_cov_24.415892 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095993 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus;s__Bariatricus comes vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737964_virus.891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139271 SAMEA13537301 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737967. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537301 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 40.6261 MAG coverage software Reads (ERR7737967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559278) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_C_22_2578__NODE_462_length_44859_cov_23.641575 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586302 sample name Hadza_MoBio_hadza-I-L_C_22_2578__NODE_462_length_44859_cov_23.641575 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737967_virus.462 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139278 SAMEA13537308 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737969. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537308 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 13.0036 MAG coverage software Reads (ERR7737969) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_D_9_2667__NODE_1440_length_33074_cov_7.420038 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586365 sample name Hadza_MoBio_hadza-I-L_D_9_2667__NODE_1440_length_33074_cov_7.420038 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738178_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737969_virus.1440 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139281 SAMEA13537311 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737970. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537311 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 8.31702 MAG coverage software Reads (ERR7737970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_H_11_1558__NODE_296_length_72613_cov_4.765813_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8837209302325582 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585812 sample name Hadza_MoBio_hadza-A-D_H_11_1558__NODE_296_length_72613_cov_4.765813_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME041878 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__CAG-1024;s__CAG-1024 sp000432015 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_provirus.296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139290 SAMEA13537320 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737971. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537320 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 50.8092 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_182_length_126191_cov_29.115895 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.6833333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_182_length_126191_cov_29.115895 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745924_bin.45 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02;s__F23-B02 sp900556535 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.182 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139293 SAMEA13537323 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7737971. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537323 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 15.4723 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_582_length_65697_cov_8.903459 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5217391304347826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_582_length_65697_cov_8.903459 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018425 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__CAG-791 sp000431495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.582 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11139308 SAMEA13537338 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7737974. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537338 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 16.1131 MAG coverage software Reads (ERR7737974) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560365) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 76 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_M_17_1798__NODE_460_length_50135_cov_8.736845_1 Viral contig found in MAG ERR7737974_bin.29 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-18 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586007 sample name Hadza_MoBio_hadza-E-H_M_17_1798__NODE_460_length_50135_cov_8.736845_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737974_provirus.460 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11139313 SAMEA13537343 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738140. BACPHLIP temperate score 0.2753052220829365 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537343 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 39.4142 MAG coverage software Reads (ERR7738140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560325) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 524 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_MoBio_hadza-E-H_O_1_1802__NODE_55_length_140753_cov_22.322585_1 Viral contig found in MAG ERR7738140_bin.12 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-18 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586011 sample name Hadza_MoBio_hadza-E-H_O_1_1802__NODE_55_length_140753_cov_22.322585_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME151566 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B;s__Ruminococcus_B gnavus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738140_provirus.55 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139326 SAMEA13537356 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738143. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537356 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 10.5651 MAG coverage software Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-I-L_K_3_2480__NODE_1402_length_38195_cov_5.831943 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586254 sample name Hadza_MoBio_hadza-I-L_K_3_2480__NODE_1402_length_38195_cov_5.831943 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745687_bin.245 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382;s__UBA6382 sp900557555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738143_virus.1402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139330 SAMEA13537360 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738144. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537360 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 141.523 MAG coverage software Reads (ERR7738144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567441) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 68 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_1_THA1057JZ__NODE_159_length_78420_cov_84.249952 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4411764705882353 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787402 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_1_THA1057JZ__NODE_159_length_78420_cov_84.249952 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268072 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella stercorea vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738144_virus.159 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139331 SAMEA13537361 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738144. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537361 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 18.353 MAG coverage software Reads (ERR7738144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567441) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_1_THA1057JZ__NODE_364_length_42505_cov_11.002852 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787402 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_1_THA1057JZ__NODE_364_length_42505_cov_11.002852 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738144_virus.364 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139341 SAMEA13537371 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738146. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537371 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 19.5062 MAG coverage software Reads (ERR7738146) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 483 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-I-L_M_24_2678__NODE_919_length_37948_cov_11.482876 Viral contig found in MAG ERR7738146_bin.51 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4482758620689655 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586376 sample name Hadza_MoBio_hadza-I-L_M_24_2678__NODE_919_length_37948_cov_11.482876 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737972_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115;s__RUG115 sp900066395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_virus.919 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139343 SAMEA13537373 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738147. BACPHLIP temperate score 0.00141699478838352 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537373 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 87.6542 MAG coverage software Reads (ERR7738147) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559941) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_B_21_1948__NODE_15_length_187820_cov_50.021977 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.54 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586087 sample name Hadza_MoBio_hadza-E-H_B_21_1948__NODE_15_length_187820_cov_50.021977 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738147_virus.15 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139345 SAMEA13537375 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738147. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537375 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 36.5791 MAG coverage software Reads (ERR7738147) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559941) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 237 Submitter Id Hadza_MoBio_hadza-E-H_B_21_1948__NODE_86_length_105151_cov_21.511687 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.43333333333333335 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586087 sample name Hadza_MoBio_hadza-E-H_B_21_1948__NODE_86_length_105151_cov_21.511687 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738147_virus.86 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139352 SAMEA13537382 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738149. BACPHLIP temperate score 0.23891699478838352 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537382 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 65.2765 MAG coverage software Reads (ERR7738149) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561419) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_C-REDO_A_10_1510__NODE_52_length_156277_cov_38.142574 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5853658536585366 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585766 sample name Hadza_MoBio_C-REDO_A_10_1510__NODE_52_length_156277_cov_38.142574 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738149_virus.52 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139356 SAMEA13537386 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7738150. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537386 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 12.9038 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_1064_length_44774_cov_7.528246 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_1064_length_44774_cov_7.528246 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738150_virus.1064 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11139364 SAMEA13537394 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738151. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537394 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 8.77976 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_1005_length_47821_cov_4.790382 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_1005_length_47821_cov_4.790382 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270871 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628;s__CAG-628 sp000438415 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738151_virus.1005 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139370 SAMEA13537400 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738152. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537400 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 23.9376 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_145_length_131934_cov_14.075885_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5853658536585366 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_145_length_131934_cov_14.075885_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_provirus.145 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139371 SAMEA13537401 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus provirus assembled from ERR7738152. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537401 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 43.9963 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_366_length_73332_cov_26.136509_1 Viral contig found in MAG ERR7738152_bin.164 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_366_length_73332_cov_26.136509_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_provirus.366 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11139378 SAMEA13537408 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738152. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537408 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 26.08 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_894_length_40459_cov_15.373904 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_894_length_40459_cov_15.373904 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_virus.894 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139380 SAMEA13537410 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738153. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537410 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 154.05 MAG coverage software Reads (ERR7738153) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559832) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-I-L_K_17_2487__NODE_425_length_36766_cov_87.779852 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586261 sample name Hadza_MoBio_hadza-I-L_K_17_2487__NODE_425_length_36766_cov_87.779852 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095938 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738153_virus.425 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139383 SAMEA13537413 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738154. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537413 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 21.3443 MAG coverage software Reads (ERR7738154) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561215) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 471 Submitter Id Hadza_MoBio_hadza-A-D_B_1_1600__NODE_77_length_102688_cov_12.310600 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.2857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585849 sample name Hadza_MoBio_hadza-A-D_B_1_1600__NODE_77_length_102688_cov_12.310600 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738154_virus.77 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139392 SAMEA13537422 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738157. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537422 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 18.1083 MAG coverage software Reads (ERR7738157) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_D_19_2669__NODE_110_length_150314_cov_10.581621_1 Viral contig found in MAG ERR7738157_bin.26 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.3 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586367 sample name Hadza_MoBio_hadza-I-L_D_19_2669__NODE_110_length_150314_cov_10.581621_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738157_provirus.110 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139399 SAMEA13537429 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738158. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537429 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 16.7517 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 113 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_314_length_90437_cov_9.846824_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9310344827586208 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_314_length_90437_cov_9.846824_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_provirus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139403 SAMEA13537433 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738158. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537433 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 29.035 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 231 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_269_length_96741_cov_16.876738 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_269_length_96741_cov_16.876738 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_virus.269 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139405 SAMEA13537435 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738158. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537435 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 21.0602 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 84 Number of CRISPR spacer hits supporting host taxonomy 1619 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_918_length_49800_cov_12.311023 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.675 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_918_length_49800_cov_12.311023 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_virus.918 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139412 SAMEA13537442 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738160. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537442 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 8.00972 MAG coverage software Reads (ERR7738160) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559708) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_P_2_2343__NODE_3410_length_16402_cov_4.554487 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586213 sample name Hadza_MoBio_hadza-E-H_P_2_2343__NODE_3410_length_16402_cov_4.554487 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.170 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900768995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738160_virus.3410 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139413 SAMEA13537443 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738160. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537443 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 14.0813 MAG coverage software Reads (ERR7738160) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559708) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 112 Submitter Id Hadza_MoBio_hadza-E-H_P_2_2343__NODE_768_length_50472_cov_8.085961 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586213 sample name Hadza_MoBio_hadza-E-H_P_2_2343__NODE_768_length_50472_cov_8.085961 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738160_virus.768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139414 SAMEA13537444 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738161. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537444 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 51.4231 MAG coverage software Reads (ERR7738161) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560062) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_B_10_2156__NODE_127_length_113956_cov_29.679739_1 Viral contig found in MAG ERR7738161_bin.25 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586142 sample name Hadza_MoBio_hadza-E-H_B_10_2156__NODE_127_length_113956_cov_29.679739_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139415 SAMEA13537445 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738161. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537445 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 29.7969 MAG coverage software Reads (ERR7738161) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560062) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 118 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-E-H_B_10_2156__NODE_717_length_42434_cov_16.962958_1 Viral contig found in MAG ERR7738161_bin.60 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586142 sample name Hadza_MoBio_hadza-E-H_B_10_2156__NODE_717_length_42434_cov_16.962958_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0307965 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139416 SAMEA13537446 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738161. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537446 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 212.743 MAG coverage software Reads (ERR7738161) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560062) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 269 Number of CRISPR spacer hits supporting host taxonomy 217 Submitter Id Hadza_MoBio_hadza-E-H_B_10_2156__NODE_173_length_97887_cov_122.101247 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586142 sample name Hadza_MoBio_hadza-E-H_B_10_2156__NODE_173_length_97887_cov_122.101247 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_virus.173 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139418 SAMEA13537448 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738161. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537448 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 20.5012 MAG coverage software Reads (ERR7738161) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560062) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-E-H_B_10_2156__NODE_654_length_44301_cov_11.739372 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; HMM-based (lower-bound) completeness score 68.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586142 sample name Hadza_MoBio_hadza-E-H_B_10_2156__NODE_654_length_44301_cov_11.739372 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_virus.436 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139419 SAMEA13537449 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738162. BACPHLIP temperate score 0.09512584798925876 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537449 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:15Z INSDC last update 2022-12-27T00:31:15Z INSDC status public MAG coverage depth 8.65886 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1789_length_35121_cov_5.225459_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1789_length_35121_cov_5.225459_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0328474 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139420 SAMEA13537450 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738162. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537450 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 10.8644 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_62_length_191983_cov_6.534772_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_62_length_191983_cov_6.534772_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_provirus.62 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139421 SAMEA13537451 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738162. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537451 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:15Z INSDC last update 2022-12-27T00:31:15Z INSDC status public MAG coverage depth 12.8108 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1132_length_47595_cov_7.167410 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1132_length_47595_cov_7.167410 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_virus.968 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139422 SAMEA13537452 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738162. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537452 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:15Z INSDC last update 2022-12-27T00:31:15Z INSDC status public MAG coverage depth 12.7828 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 201 Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1476_length_39926_cov_7.885844 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1476_length_39926_cov_7.885844 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1476 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139424 SAMEA13537454 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738162. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537454 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 9.20783 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_2659_length_26113_cov_5.555308 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_2659_length_26113_cov_5.555308 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.328 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139425 SAMEA13537455 1701671 uncultured podovirus This sample represents an uncultured CrAss-like virus sp. virus assembled from ERR7738162. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537455 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 36.0008 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_342_length_92480_cov_20.643074 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_342_length_92480_cov_20.643074 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; CrAss-like virus sp. virus enrichment approach none ERS11139426 SAMEA13537456 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738162. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537456 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 16.0631 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_4694_length_16150_cov_9.721209 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; ITR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_4694_length_16150_cov_9.721209 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.6231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139427 SAMEA13537457 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738162. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537457 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 9.10895 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 239 Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_709_length_62392_cov_5.124529 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.5405405405405406 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_709_length_62392_cov_5.124529 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.861 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139428 SAMEA13537458 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738162. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537458 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 6.86949 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_9650_length_8318_cov_3.929256 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_9650_length_8318_cov_3.929256 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.9650 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11139429 SAMEA13537459 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738163. BACPHLIP temperate score 0.525 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537459 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 197.531 MAG coverage software Reads (ERR7738163) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_D_10_2185__NODE_201_length_101965_cov_152.782339_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_MoBio_hadza-E-H_D_10_2185__NODE_201_length_101965_cov_152.782339_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.3646 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139430 SAMEA13537460 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus provirus assembled from ERR7738163. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537460 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 8.88592 MAG coverage software Reads (ERR7738163) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_D_10_2185__NODE_955_length_44372_cov_5.079038_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_MoBio_hadza-E-H_D_10_2185__NODE_955_length_44372_cov_5.079038_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.2677 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11139431 SAMEA13537461 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738163. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537461 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 33.2563 MAG coverage software Reads (ERR7738163) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_D_10_2185__NODE_17_length_267745_cov_20.190938 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.8412698412698413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_MoBio_hadza-E-H_D_10_2185__NODE_17_length_267745_cov_20.190938 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.47 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139433 SAMEA13537463 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738164. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537463 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 11.7116 MAG coverage software Reads (ERR7738164) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561040) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_F_15_1568__NODE_110_length_65240_cov_6.063011_1_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585822 sample name Hadza_MoBio_hadza-A-D_F_15_1568__NODE_110_length_65240_cov_6.063011_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738164_provirus.110 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139434 SAMEA13537464 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738164. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537464 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 29.0937 MAG coverage software Reads (ERR7738164) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561040) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-A-D_F_15_1568__NODE_1817_length_13774_cov_11.362862 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585822 sample name Hadza_MoBio_hadza-A-D_F_15_1568__NODE_1817_length_13774_cov_11.362862 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738164_virus.1817 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139287 SAMEA13537317 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7737971. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537317 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:38Z INSDC last update 2022-12-26T20:28:38Z INSDC status public MAG coverage depth 46.8431 MAG coverage software Reads (ERR7737971) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_F_5_2654__NODE_1080_length_42361_cov_26.958140 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586355 sample name Hadza_MoBio_hadza-I-L_F_5_2654__NODE_1080_length_42361_cov_26.958140 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746398_bin.161 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;s__Oribacterium sp900772695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139327 SAMEA13537357 336724 Myoviridae environmental samples This sample represents an uncultured Bdellovibrio phage phi1422 virus assembled from ERR7738143. BACPHLIP temperate score 0.12261836275922892 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537357 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 7.17195 MAG coverage software Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_K_3_2480__NODE_2655_length_21947_cov_3.836671 Viral contig found in MAG ERR7738143_bin.153 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586254 sample name Hadza_MoBio_hadza-I-L_K_3_2480__NODE_2655_length_21947_cov_3.836671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_virus.2404 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Bdellovibrio phage phi1422 virus enrichment approach none ERS11139332 SAMEA13537362 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738145. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537362 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:39Z INSDC last update 2022-12-26T20:28:39Z INSDC status public MAG coverage depth 10.6475 MAG coverage software Reads (ERR7738145) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559588) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 145 Submitter Id Hadza_MoBio_hadza-E-H_J_24_2316__NODE_335_length_82112_cov_6.260182_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586188 sample name Hadza_MoBio_hadza-E-H_J_24_2316__NODE_335_length_82112_cov_6.260182_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11139333 SAMEA13537363 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738145. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537363 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 14.6113 MAG coverage software Reads (ERR7738145) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559588) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_J_24_2316__NODE_1338_length_29662_cov_8.948623 Viral contig found in MAG ERR7738145_bin.67 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586188 sample name Hadza_MoBio_hadza-E-H_J_24_2316__NODE_1338_length_29662_cov_8.948623 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME029635 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417;s__CAG-417 sp000432835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.1296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139335 SAMEA13537365 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738145. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537365 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 34.6269 MAG coverage software Reads (ERR7738145) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559588) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_J_24_2316__NODE_800_length_45056_cov_21.645168 Viral contig found in MAG ERR7738145_bin.85 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586188 sample name Hadza_MoBio_hadza-E-H_J_24_2316__NODE_800_length_45056_cov_21.645168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747615_virus.1414 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139338 SAMEA13537368 2133760 Siphoviridae environmental samples This sample represents an uncultured Vegasvirus virus assembled from ERR7738146. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537368 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 6.79443 MAG coverage software Reads (ERR7738146) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-I-L_M_24_2678__NODE_1603_length_24876_cov_3.789024 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586376 sample name Hadza_MoBio_hadza-I-L_M_24_2678__NODE_1603_length_24876_cov_3.789024 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME266163 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;s__Lachnospira sp900316325 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_virus.1603 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Gochnauervirinae; Vegasvirus virus enrichment approach none ERS11139344 SAMEA13537374 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738147. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537374 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 14.8734 MAG coverage software Reads (ERR7738147) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559941) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-E-H_B_21_1948__NODE_339_length_56156_cov_8.617415 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586087 sample name Hadza_MoBio_hadza-E-H_B_21_1948__NODE_339_length_56156_cov_8.617415 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_virus.1035 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139348 SAMEA13537378 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738148. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537378 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 12.8461 MAG coverage software Reads (ERR7738148) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559582) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_J_18_2314__NODE_804_length_41411_cov_7.292858 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586186 sample name Hadza_MoBio_hadza-E-H_J_18_2314__NODE_804_length_41411_cov_7.292858 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738169_virus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139360 SAMEA13537390 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738150. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537390 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 49.6527 MAG coverage software Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-E-H_F_10_2221__NODE_429_length_83754_cov_29.753050 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586158 sample name Hadza_MoBio_hadza-E-H_F_10_2221__NODE_429_length_83754_cov_29.753050 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738150_virus.429 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139362 SAMEA13537392 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738151. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537392 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 11.4524 MAG coverage software Reads (ERR7738151) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560211) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_16_2233__NODE_114_length_165305_cov_6.462694_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_MoBio_hadza-E-H_F_16_2233__NODE_114_length_165305_cov_6.462694_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738150_virus.112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139382 SAMEA13537412 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738154. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537412 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 50.0154 MAG coverage software Reads (ERR7738154) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561215) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_B_1_1600__NODE_1244_length_23841_cov_31.406497 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585849 sample name Hadza_MoBio_hadza-A-D_B_1_1600__NODE_1244_length_23841_cov_31.406497 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.2254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11139389 SAMEA13537419 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738156. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537419 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:41Z INSDC last update 2022-12-26T20:28:41Z INSDC status public MAG coverage depth 18.8981 MAG coverage software Reads (ERR7738156) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559605) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_J_10_2310__NODE_700_length_43357_cov_11.300601_1 Viral contig found in MAG ERR7738156_bin.81 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586182 sample name Hadza_MoBio_hadza-E-H_J_10_2310__NODE_700_length_43357_cov_11.300601_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_virus.319 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139400 SAMEA13537430 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738158. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537430 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:42Z INSDC last update 2022-12-26T20:28:42Z INSDC status public MAG coverage depth 37.6744 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_527_length_69202_cov_22.280260_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5757575757575758 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_527_length_69202_cov_22.280260_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745743_virus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139231 SAMEA13537261 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7737607. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537261 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 34.097 MAG coverage software Reads (ERR7737607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_C-REDO_E_6_1557__NODE_18_length_59667_cov_19.689965 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4893617021276595 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_MoBio_C-REDO_E_6_1557__NODE_18_length_59667_cov_19.689965 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737607_virus.18 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139232 SAMEA13537262 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7737617. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537262 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 56.5137 MAG coverage software Reads (ERR7737617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560303) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_MoBio_hadza-E-H_K_19_1779__NODE_162_length_59640_cov_32.245589 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586001 sample name Hadza_MoBio_hadza-E-H_K_19_1779__NODE_162_length_59640_cov_32.245589 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737617_virus.162 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139246 SAMEA13537276 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7737955. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537276 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 14.9743 MAG coverage software Reads (ERR7737955) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560488) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 422 Number of CRISPR spacer hits supporting host taxonomy 249 Submitter Id Hadza_MoBio_F_H_7_1932__NODE_147_length_67774_cov_7.743726_1 Viral contig found in MAG ERR7737955_bin.26 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586073 sample name Hadza_MoBio_F_H_7_1932__NODE_147_length_67774_cov_7.743726_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737955_provirus.147 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139300 SAMEA13537330 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7737972. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537330 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:22Z INSDC last update 2022-12-27T19:09:22Z INSDC status public MAG coverage depth 25.0264 MAG coverage software Reads (ERR7737972) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560076) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_B_8_2155__NODE_70_length_217453_cov_13.820661 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 19 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586141 sample name Hadza_MoBio_hadza-E-H_B_8_2155__NODE_70_length_217453_cov_13.820661 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737972_virus.70 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139339 SAMEA13537369 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738146. BACPHLIP temperate score 0.01328965839962564 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537369 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 106.39 MAG coverage software Reads (ERR7738146) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_M_24_2678__NODE_35_length_192140_cov_62.729386 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.5423728813559322 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586376 sample name Hadza_MoBio_hadza-I-L_M_24_2678__NODE_35_length_192140_cov_62.729386 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_virus.35 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139375 SAMEA13537405 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738152. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537405 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 198.477 MAG coverage software Reads (ERR7738152) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561091) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_D_1_1586__NODE_36_length_238499_cov_101.425292 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.4696969696969697 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585835 sample name Hadza_MoBio_hadza-A-D_D_1_1586__NODE_36_length_238499_cov_101.425292 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_virus.36 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139401 SAMEA13537431 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738158. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537431 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 294.568 MAG coverage software Reads (ERR7738158) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_D_18_2193__NODE_1296_length_40453_cov_167.289900 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586151 sample name Hadza_MoBio_hadza-E-H_D_18_2193__NODE_1296_length_40453_cov_167.289900 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_virus.1296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139417 SAMEA13537447 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738161. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537447 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 103.295 MAG coverage software Reads (ERR7738161) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560062) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_B_10_2156__NODE_317_length_68956_cov_58.269894 Viral contig found in MAG ERR7738161_bin.74 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586142 sample name Hadza_MoBio_hadza-E-H_B_10_2156__NODE_317_length_68956_cov_58.269894 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_virus.317 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139423 SAMEA13537453 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738162. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537453 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:15Z INSDC last update 2022-12-27T00:31:15Z INSDC status public MAG coverage depth 50.7801 MAG coverage software Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1734_length_35883_cov_30.318354 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586157 sample name Hadza_MoBio_hadza-E-H_F_8_2217__NODE_1734_length_35883_cov_30.318354 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738568_bin.326 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__SFEL01;s__SFEL01 sp004557245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.1393 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139432 SAMEA13537462 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738163. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537462 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 15.7046 MAG coverage software Reads (ERR7738163) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 174 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_D_10_2185__NODE_607_length_59834_cov_9.273022 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_MoBio_hadza-E-H_D_10_2185__NODE_607_length_59834_cov_9.273022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372372 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139435 SAMEA13537465 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7738164. BACPHLIP temperate score 0.10135789431064383 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537465 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 13.4141 MAG coverage software Reads (ERR7738164) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561040) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_F_15_1568__NODE_45_length_95683_cov_6.324352 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9382716049382716 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585822 sample name Hadza_MoBio_hadza-A-D_F_15_1568__NODE_45_length_95683_cov_6.324352 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.225 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11139436 SAMEA13537466 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738165. BACPHLIP temperate score 0.675 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537466 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 234.517 MAG coverage software Reads (ERR7738165) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559683) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_N_24_2342__NODE_293_length_76219_cov_141.046820_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.25 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586212 sample name Hadza_MoBio_hadza-E-H_N_24_2342__NODE_293_length_76219_cov_141.046820_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0347583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139437 SAMEA13537467 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738165. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537467 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 219.558 MAG coverage software Reads (ERR7738165) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559683) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 223 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-E-H_N_24_2342__NODE_75_length_129618_cov_129.412881_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 82.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586212 sample name Hadza_MoBio_hadza-E-H_N_24_2342__NODE_75_length_129618_cov_129.412881_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139438 SAMEA13537468 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738165. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537468 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 22.6296 MAG coverage software Reads (ERR7738165) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559683) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 158 Submitter Id Hadza_MoBio_hadza-E-H_N_24_2342__NODE_143_length_103862_cov_13.319950 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586212 sample name Hadza_MoBio_hadza-E-H_N_24_2342__NODE_143_length_103862_cov_13.319950 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745410_virus.278 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139439 SAMEA13537469 2100421 uncultured Caudovirales phage This sample represents an uncultured Schitoviridae virus assembled from ERR7738165. BACPHLIP temperate score 0.06303277487972782 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537469 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 30.0031 MAG coverage software Reads (ERR7738165) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559683) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 332 Submitter Id Hadza_MoBio_hadza-E-H_N_24_2342__NODE_316_length_73969_cov_18.264305 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586212 sample name Hadza_MoBio_hadza-E-H_N_24_2342__NODE_316_length_73969_cov_18.264305 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738189_virus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Schitoviridae virus enrichment approach none ERS11139440 SAMEA13537470 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738166. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537470 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 13.5434 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_121_length_174784_cov_8.223082_1 Viral contig found in MAG ERR7738166_bin.148 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7407407407407407 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_121_length_174784_cov_8.223082_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140320 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A sp000436615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_provirus.121 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139441 SAMEA13537471 1701671 uncultured podovirus This sample represents an uncultured Uetakevirus provirus assembled from ERR7738166. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537471 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 9.39735 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9289 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_295_length_116149_cov_5.433653_1 Viral contig found in MAG ERR7738166_bin.157 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5192307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_295_length_116149_cov_5.433653_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_provirus.295 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Uetakevirus virus enrichment approach none ERS11139442 SAMEA13537472 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738166. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537472 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 18.3141 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 83 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_1011_length_55614_cov_11.502152 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8979591836734694 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_1011_length_55614_cov_11.502152 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_virus.1011 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139443 SAMEA13537473 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738166. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537473 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 75.6946 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_1516_length_40995_cov_43.899237 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_1516_length_40995_cov_43.899237 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_virus.1516 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139444 SAMEA13537474 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738166. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537474 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 24.6029 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 144 Number of CRISPR spacer hits supporting host taxonomy 147 Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_1669_length_37732_cov_14.458903 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6176470588235294 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_1669_length_37732_cov_14.458903 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0341321 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139445 SAMEA13537475 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738166. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537475 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 19.6959 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_2779_length_23669_cov_12.829561 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_2779_length_23669_cov_12.829561 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257483 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__UBA644;g__UBA644;s__UBA644 sp900547165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745398_provirus.103 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139446 SAMEA13537476 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738166. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537476 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 7.19837 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_4516_length_15465_cov_4.132376 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_4516_length_15465_cov_4.132376 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_virus.4516 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139447 SAMEA13537477 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738166. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537477 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 36.9212 MAG coverage software Reads (ERR7738166) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560179) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 199 Submitter Id Hadza_MoBio_hadza-E-H_D_24_2201__NODE_850_length_61675_cov_21.902919 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586153 sample name Hadza_MoBio_hadza-E-H_D_24_2201__NODE_850_length_61675_cov_21.902919 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.604 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139448 SAMEA13537478 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738167. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537478 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 50.8626 MAG coverage software Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 191 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-I-L_B_9_2646__NODE_263_length_109236_cov_30.475059_1 Viral contig found in MAG ERR7738167_bin.176 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586350 sample name Hadza_MoBio_hadza-I-L_B_9_2646__NODE_263_length_109236_cov_30.475059_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_provirus.117 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139449 SAMEA13537479 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7738167. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537479 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 10.8527 MAG coverage software Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-I-L_B_9_2646__NODE_761_length_59458_cov_6.284771_1 Viral contig found in MAG ERR7738167_bin.91 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586350 sample name Hadza_MoBio_hadza-I-L_B_9_2646__NODE_761_length_59458_cov_6.284771_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738167_provirus.761 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11139450 SAMEA13537480 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738167. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537480 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 12.8345 MAG coverage software Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-I-L_B_9_2646__NODE_1198_length_43406_cov_7.406864 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586350 sample name Hadza_MoBio_hadza-I-L_B_9_2646__NODE_1198_length_43406_cov_7.406864 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251925 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__RUG472;s__RUG472 sp900545265 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738167_virus.1198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139451 SAMEA13537481 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7738167. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537481 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 9.38275 MAG coverage software Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 89 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-I-L_B_9_2646__NODE_1716_length_33681_cov_5.212147 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586350 sample name Hadza_MoBio_hadza-I-L_B_9_2646__NODE_1716_length_33681_cov_5.212147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_virus.231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11139452 SAMEA13537482 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738167. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537482 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 13.9124 MAG coverage software Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_B_9_2646__NODE_2453_length_25732_cov_8.098187 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586350 sample name Hadza_MoBio_hadza-I-L_B_9_2646__NODE_2453_length_25732_cov_8.098187 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139453 SAMEA13537483 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738167. BACPHLIP temperate score 0.04343334073279703 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537483 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 31.2471 MAG coverage software Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 112 Number of CRISPR spacer hits supporting host taxonomy 273 Submitter Id Hadza_MoBio_hadza-I-L_B_9_2646__NODE_4178_length_16496_cov_18.101285 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586350 sample name Hadza_MoBio_hadza-I-L_B_9_2646__NODE_4178_length_16496_cov_18.101285 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11139454 SAMEA13537484 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738167. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537484 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 230.488 MAG coverage software Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-I-L_B_9_2646__NODE_6656_length_10867_cov_135.223262 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586350 sample name Hadza_MoBio_hadza-I-L_B_9_2646__NODE_6656_length_10867_cov_135.223262 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.12584 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11139455 SAMEA13537485 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7738168. BACPHLIP temperate score 0.14888717346443942 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537485 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 11.0061 MAG coverage software Reads (ERR7738168) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 110 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_C-REDO_A_11_1511__NODE_636_length_50443_cov_6.059385_1 Viral contig found in MAG ERR7738168_bin.33 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585767 sample name Hadza_MoBio_C-REDO_A_11_1511__NODE_636_length_50443_cov_6.059385_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_provirus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11139456 SAMEA13537486 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738168. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537486 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 14.6105 MAG coverage software Reads (ERR7738168) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_A_11_1511__NODE_1364_length_28853_cov_8.746942 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585767 sample name Hadza_MoBio_C-REDO_A_11_1511__NODE_1364_length_28853_cov_8.746942 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738581_bin.271 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745408_virus.974 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139457 SAMEA13537487 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738168. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537487 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 15.5783 MAG coverage software Reads (ERR7738168) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_C-REDO_A_11_1511__NODE_2772_length_17140_cov_8.516849 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585767 sample name Hadza_MoBio_C-REDO_A_11_1511__NODE_2772_length_17140_cov_8.516849 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.4145 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139458 SAMEA13537488 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738168. BACPHLIP temperate score 0.06433820478765558 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537488 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 11.8888 MAG coverage software Reads (ERR7738168) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_C-REDO_A_11_1511__NODE_61_length_181164_cov_6.580715 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 17 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585767 sample name Hadza_MoBio_C-REDO_A_11_1511__NODE_61_length_181164_cov_6.580715 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024263 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides sp900549585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139459 SAMEA13537489 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738168. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537489 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 36.1916 MAG coverage software Reads (ERR7738168) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_C-REDO_A_11_1511__NODE_851_length_40662_cov_20.454823 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585767 sample name Hadza_MoBio_C-REDO_A_11_1511__NODE_851_length_40662_cov_20.454823 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_virus.1078 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139460 SAMEA13537490 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738169. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537490 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 17.8845 MAG coverage software Reads (ERR7738169) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 157 Submitter Id Hadza_MoBio_hadza-I-L_M_15_2497__NODE_30_length_237824_cov_10.176549_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586271 sample name Hadza_MoBio_hadza-I-L_M_15_2497__NODE_30_length_237824_cov_10.176549_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11139461 SAMEA13537491 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738169. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537491 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 8.29767 MAG coverage software Reads (ERR7738169) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_M_15_2497__NODE_944_length_36049_cov_4.635883_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586271 sample name Hadza_MoBio_hadza-I-L_M_15_2497__NODE_944_length_36049_cov_4.635883_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747615_virus.2042 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139462 SAMEA13537492 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738169. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537492 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 72.9325 MAG coverage software Reads (ERR7738169) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_M_15_2497__NODE_392_length_70568_cov_43.207941 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586271 sample name Hadza_MoBio_hadza-I-L_M_15_2497__NODE_392_length_70568_cov_43.207941 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738155_virus.49 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139463 SAMEA13537493 926697 uncultured Microviridae This sample represents an uncultured unclassified Microviridae virus assembled from ERR7738169. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537493 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 6.76676 MAG coverage software Reads (ERR7738169) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_M_15_2497__NODE_6535_length_5432_cov_4.025210 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586271 sample name Hadza_MoBio_hadza-I-L_M_15_2497__NODE_6535_length_5432_cov_4.025210 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747615_virus.16257 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae virus enrichment approach none ERS11139464 SAMEA13537494 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738170. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537494 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 311.497 MAG coverage software Reads (ERR7738170) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_B_5_2673__NODE_27_length_239812_cov_177.582743_1 Viral contig found in MAG ERR7738170_bin.69 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; HMM-based (lower-bound) completeness score 55.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586371 sample name Hadza_MoBio_hadza-I-L_B_5_2673__NODE_27_length_239812_cov_177.582743_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738612_bin.275 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_provirus.43 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139465 SAMEA13537495 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738170. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537495 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 9.48661 MAG coverage software Reads (ERR7738170) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_B_5_2673__NODE_705_length_56096_cov_5.401096_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586371 sample name Hadza_MoBio_hadza-I-L_B_5_2673__NODE_705_length_56096_cov_5.401096_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091228 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900549865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738612_provirus.660 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139466 SAMEA13537496 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr131_1 virus assembled from ERR7738170. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537496 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 20.4474 MAG coverage software Reads (ERR7738170) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_B_5_2673__NODE_1357_length_36859_cov_11.853869 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586371 sample name Hadza_MoBio_hadza-I-L_B_5_2673__NODE_1357_length_36859_cov_11.853869 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.967 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr131_1 virus enrichment approach none ERS11139468 SAMEA13537498 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738170. BACPHLIP temperate score 0.04730176211453744 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537498 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 10.5561 MAG coverage software Reads (ERR7738170) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_B_5_2673__NODE_823_length_50612_cov_5.825745 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8529411764705882 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586371 sample name Hadza_MoBio_hadza-I-L_B_5_2673__NODE_823_length_50612_cov_5.825745 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738612_virus.1007 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139469 SAMEA13537499 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738171. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537499 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 19.2748 MAG coverage software Reads (ERR7738171) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 318 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-I-L_O_6_2676__NODE_359_length_78261_cov_11.081922_1 Viral contig found in MAG ERR7738171_bin.8 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586374 sample name Hadza_MoBio_hadza-I-L_O_6_2676__NODE_359_length_78261_cov_11.081922_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095983 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;s__Mediterraneibacter lactaris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737968_provirus.496 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139470 SAMEA13537500 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738171. BACPHLIP temperate score 0.1128166006446914 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537500 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 17.1787 MAG coverage software Reads (ERR7738171) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 208 Submitter Id Hadza_MoBio_hadza-I-L_O_6_2676__NODE_1176_length_23550_cov_9.972607 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586374 sample name Hadza_MoBio_hadza-I-L_O_6_2676__NODE_1176_length_23550_cov_9.972607 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_provirus.1602 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139471 SAMEA13537501 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738171. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537501 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 19.6773 MAG coverage software Reads (ERR7738171) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 144 Submitter Id Hadza_MoBio_hadza-I-L_O_6_2676__NODE_799_length_36503_cov_11.299127 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586374 sample name Hadza_MoBio_hadza-I-L_O_6_2676__NODE_799_length_36503_cov_11.299127 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0325958 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139472 SAMEA13537502 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738172. BACPHLIP temperate score 0.05270140052539582 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537502 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 142.664 MAG coverage software Reads (ERR7738172) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_D_1_2641__NODE_329_length_81574_cov_87.458446_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586345 sample name Hadza_MoBio_hadza-I-L_D_1_2641__NODE_329_length_81574_cov_87.458446_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139473 SAMEA13537503 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738172. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537503 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 11.0947 MAG coverage software Reads (ERR7738172) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 171 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_D_1_2641__NODE_1008_length_42297_cov_6.176646 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; HMM-based (lower-bound) completeness score 81.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586345 sample name Hadza_MoBio_hadza-I-L_D_1_2641__NODE_1008_length_42297_cov_6.176646 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139474 SAMEA13537504 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738172. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537504 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 37.8967 MAG coverage software Reads (ERR7738172) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 363 Submitter Id Hadza_MoBio_hadza-I-L_D_1_2641__NODE_160_length_110118_cov_21.802728 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.627906976744186 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586345 sample name Hadza_MoBio_hadza-I-L_D_1_2641__NODE_160_length_110118_cov_21.802728 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019375 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R;s__Eubacterium_R sp000436835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738172_virus.160 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11139476 SAMEA13537506 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738172. BACPHLIP temperate score 0.6824339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537506 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 265.253 MAG coverage software Reads (ERR7738172) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_MoBio_hadza-I-L_D_1_2641__NODE_525_length_63351_cov_148.943847 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586345 sample name Hadza_MoBio_hadza-I-L_D_1_2641__NODE_525_length_63351_cov_148.943847 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.131 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139477 SAMEA13537507 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738172. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537507 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 35.9599 MAG coverage software Reads (ERR7738172) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 119 Submitter Id Hadza_MoBio_hadza-I-L_D_1_2641__NODE_856_length_46842_cov_20.578403 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586345 sample name Hadza_MoBio_hadza-I-L_D_1_2641__NODE_856_length_46842_cov_20.578403 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_virus.471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139478 SAMEA13537508 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738173. BACPHLIP temperate score 0.1674559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537508 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 71.6433 MAG coverage software Reads (ERR7738173) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-I-L_B_4_1344__NODE_163_length_98526_cov_40.229591_1 Viral contig found in MAG ERR7738173_bin.9 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_B_4_1344__NODE_163_length_98526_cov_40.229591_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738246_provirus.125 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139479 SAMEA13537509 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738173. BACPHLIP temperate score 0.15495594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537509 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 215.37 MAG coverage software Reads (ERR7738173) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 337 Submitter Id Hadza_MoBio_hadza-I-L_B_4_1344__NODE_98_length_124484_cov_124.072785_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_B_4_1344__NODE_98_length_124484_cov_124.072785_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738153_virus.426 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139480 SAMEA13537510 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738173. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537510 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 189.44 MAG coverage software Reads (ERR7738173) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 148 Submitter Id Hadza_MoBio_hadza-I-L_B_4_1344__NODE_522_length_45203_cov_107.837898 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_B_4_1344__NODE_522_length_45203_cov_107.837898 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738173_virus.522 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139482 SAMEA13537512 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738174. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537512 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 11.6113 MAG coverage software Reads (ERR7738174) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560999) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_E_12_1563__NODE_83_length_180035_cov_6.616438_1 Viral contig found in MAG ERR7738174_bin.70 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585817 sample name Hadza_MoBio_C-REDO_E_12_1563__NODE_83_length_180035_cov_6.616438_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738559_bin.129 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_provirus.1362 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139483 SAMEA13537513 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738174. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537513 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 49.3623 MAG coverage software Reads (ERR7738174) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560999) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_C-REDO_E_12_1563__NODE_1135_length_38728_cov_28.199658 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585817 sample name Hadza_MoBio_C-REDO_E_12_1563__NODE_1135_length_38728_cov_28.199658 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737954_virus.81 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139484 SAMEA13537514 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738174. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537514 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 12.7443 MAG coverage software Reads (ERR7738174) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560999) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_C-REDO_E_12_1563__NODE_1277_length_35183_cov_7.250812 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585817 sample name Hadza_MoBio_C-REDO_E_12_1563__NODE_1277_length_35183_cov_7.250812 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738174_virus.1277 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139485 SAMEA13537515 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738174. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537515 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 45.9432 MAG coverage software Reads (ERR7738174) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560999) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 167 Submitter Id Hadza_MoBio_C-REDO_E_12_1563__NODE_259_length_100221_cov_26.571257 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585817 sample name Hadza_MoBio_C-REDO_E_12_1563__NODE_259_length_100221_cov_26.571257 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.209 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139486 SAMEA13537516 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738174. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537516 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 12.8864 MAG coverage software Reads (ERR7738174) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560999) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 88 Submitter Id Hadza_MoBio_C-REDO_E_12_1563__NODE_659_length_56188_cov_7.245210 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; HMM-based (lower-bound) completeness score 51.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585817 sample name Hadza_MoBio_C-REDO_E_12_1563__NODE_659_length_56188_cov_7.245210 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738174_virus.659 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139487 SAMEA13537517 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738175. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537517 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 84.1822 MAG coverage software Reads (ERR7738175) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 884 Submitter Id Hadza_MoBio_hadza-I-L_H_24_1254__NODE_14_length_335182_cov_48.927566_1 Viral contig found in MAG ERR7738175_bin.39 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9666666666666668 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585672 sample name Hadza_MoBio_hadza-I-L_H_24_1254__NODE_14_length_335182_cov_48.927566_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738226_virus.423 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139488 SAMEA13537518 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738175. BACPHLIP temperate score 0.5399779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537518 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 69.3933 MAG coverage software Reads (ERR7738175) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2092 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_H_24_1254__NODE_552_length_39029_cov_40.394383 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6136363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585672 sample name Hadza_MoBio_hadza-I-L_H_24_1254__NODE_552_length_39029_cov_40.394383 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0271284 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139489 SAMEA13537519 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738176. BACPHLIP temperate score 0.02736784140969162 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537519 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 14.7142 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_2291_length_24661_cov_8.930076_1 Viral contig found in MAG ERR7738176_bin.191 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_2291_length_24661_cov_8.930076_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger variabilis_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745556_provirus.786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139491 SAMEA13537521 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738176. BACPHLIP temperate score 0.03469162995594714 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537521 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 8.69798 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_1391_length_34148_cov_4.947345 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_1391_length_34148_cov_4.947345 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_virus.1391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139492 SAMEA13537522 2133760 Siphoviridae environmental samples This sample represents an uncultured Teubervirus virus assembled from ERR7738176. BACPHLIP temperate score 0.09419107100014808 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537522 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 23.4325 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_2033_length_26918_cov_13.710741 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_2033_length_26918_cov_13.710741 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Teubervirus virus enrichment approach none ERS11139493 SAMEA13537523 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738176. BACPHLIP temperate score 0.16375920696193652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537523 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 37.7082 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_2878_length_21159_cov_21.853382 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_2878_length_21159_cov_21.853382 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.3747 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139494 SAMEA13537524 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738176. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537524 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 6.32103 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_4194_length_16211_cov_3.646275 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_4194_length_16211_cov_3.646275 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_provirus.1546 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139495 SAMEA13537525 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738176. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537525 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 43.8037 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 153 Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_583_length_55609_cov_25.826442 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.32 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_583_length_55609_cov_25.826442 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_virus.583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139497 SAMEA13537527 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738177. BACPHLIP temperate score 0.4125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537527 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 17.3222 MAG coverage software Reads (ERR7738177) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_I_4_1118__NODE_229_length_108777_cov_10.167829_1 Viral contig found in MAG ERR7738177_bin.180 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585542 sample name Hadza_MoBio_hadza-A-D_I_4_1118__NODE_229_length_108777_cov_10.167829_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_provirus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139498 SAMEA13537528 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738177. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537528 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 50.5347 MAG coverage software Reads (ERR7738177) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_I_4_1118__NODE_579_length_64655_cov_29.358249_1 Viral contig found in MAG ERR7738177_bin.104 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 75.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585542 sample name Hadza_MoBio_hadza-A-D_I_4_1118__NODE_579_length_64655_cov_29.358249_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_provirus.784 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139499 SAMEA13537529 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738177. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537529 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 10.0654 MAG coverage software Reads (ERR7738177) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 170 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_MoBio_hadza-A-D_I_4_1118__NODE_1258_length_39268_cov_5.747212 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 74.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585542 sample name Hadza_MoBio_hadza-A-D_I_4_1118__NODE_1258_length_39268_cov_5.747212 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139500 SAMEA13537530 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738177. BACPHLIP temperate score 0.7449339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537530 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 8.37117 MAG coverage software Reads (ERR7738177) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_I_4_1118__NODE_2118_length_26208_cov_4.653438 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585542 sample name Hadza_MoBio_hadza-A-D_I_4_1118__NODE_2118_length_26208_cov_4.653438 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745990_bin.104 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1731;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_virus.2118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139501 SAMEA13537531 2100421 uncultured Caudovirales phage This sample represents an uncultured Picovirinae virus assembled from ERR7738177. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537531 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 21.3291 MAG coverage software Reads (ERR7738177) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_I_4_1118__NODE_3108_length_18198_cov_12.204017 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 58.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585542 sample name Hadza_MoBio_hadza-A-D_I_4_1118__NODE_3108_length_18198_cov_12.204017 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.118 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A;s__Coprococcus_A sp900548825 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_virus.3141 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae; Picovirinae virus enrichment approach none ERS11139502 SAMEA13537532 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738177. BACPHLIP temperate score 0.06334385272040957 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537532 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 12.8244 MAG coverage software Reads (ERR7738177) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_I_4_1118__NODE_616_length_62408_cov_7.229228 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585542 sample name Hadza_MoBio_hadza-A-D_I_4_1118__NODE_616_length_62408_cov_7.229228 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.696 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139504 SAMEA13537534 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738178. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537534 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 17.8425 MAG coverage software Reads (ERR7738178) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559934) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-I-L_M_23_2501__NODE_1027_length_41670_cov_10.440916 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586275 sample name Hadza_MoBio_hadza-I-L_M_23_2501__NODE_1027_length_41670_cov_10.440916 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0316936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139505 SAMEA13537535 340016 uncultured virus This sample represents an uncultured Pseudomonas phage PPAT virus assembled from ERR7738178. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537535 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 18.6164 MAG coverage software Reads (ERR7738178) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559934) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_M_23_2501__NODE_1321_length_34899_cov_10.757434 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586275 sample name Hadza_MoBio_hadza-I-L_M_23_2501__NODE_1321_length_34899_cov_10.757434 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0240361 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Pseudomonas phage PPAT virus enrichment approach none ERS11139506 SAMEA13537536 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738178. BACPHLIP temperate score 0.864977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537536 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 222.294 MAG coverage software Reads (ERR7738178) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559934) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_M_23_2501__NODE_1987_length_25649_cov_129.932700 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586275 sample name Hadza_MoBio_hadza-I-L_M_23_2501__NODE_1987_length_25649_cov_129.932700 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139507 SAMEA13537537 2100421 uncultured Caudovirales phage This sample represents an uncultured Schitoviridae virus assembled from ERR7738178. BACPHLIP temperate score 0.06303277487972782 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537537 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 22.6133 MAG coverage software Reads (ERR7738178) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559934) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 332 Submitter Id Hadza_MoBio_hadza-I-L_M_23_2501__NODE_397_length_73969_cov_13.424755 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586275 sample name Hadza_MoBio_hadza-I-L_M_23_2501__NODE_397_length_73969_cov_13.424755 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738189_virus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Schitoviridae virus enrichment approach none ERS11139508 SAMEA13537538 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738178. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537538 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 10.1276 MAG coverage software Reads (ERR7738178) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559934) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_M_23_2501__NODE_606_length_57816_cov_5.782210 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.96875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586275 sample name Hadza_MoBio_hadza-I-L_M_23_2501__NODE_606_length_57816_cov_5.782210 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738233_virus.173 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139510 SAMEA13537540 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738179. BACPHLIP temperate score 0.11497797356828196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537540 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 21.7404 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_219_length_131503_cov_12.372149_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_219_length_131503_cov_12.372149_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139511 SAMEA13537541 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738179. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537541 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 225.114 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_508_length_84361_cov_127.862690_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_508_length_84361_cov_127.862690_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_provirus.587 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139512 SAMEA13537542 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738179. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537542 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 16.0357 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_931_length_58305_cov_9.292626_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_931_length_58305_cov_9.292626_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.242 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139513 SAMEA13537543 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738179. BACPHLIP temperate score 0.902477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537543 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 15.6572 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_1464_length_40970_cov_8.834153 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_1464_length_40970_cov_8.834153 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_virus.1418 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139514 SAMEA13537544 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738179. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537544 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 12.3507 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_2047_length_31085_cov_7.137835 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_2047_length_31085_cov_7.137835 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-917;g__CAG-475;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_provirus.161 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139515 SAMEA13537545 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738179. BACPHLIP temperate score 0.08777445863796453 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537545 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 158.02 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_344_length_105495_cov_89.615768 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.972972972972973 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_344_length_105495_cov_89.615768 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11139516 SAMEA13537546 2100421 uncultured Caudovirales phage This sample represents an uncultured Schitoviridae virus assembled from ERR7738179. BACPHLIP temperate score 0.11513032049760293 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537546 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 9.33734 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 325 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_610_length_74941_cov_5.316494 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_610_length_74941_cov_5.316494 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.669 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Schitoviridae virus enrichment approach none ERS11139517 SAMEA13537547 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738179. BACPHLIP temperate score 0.525 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537547 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 8.29569 MAG coverage software Reads (ERR7738179) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_K_7_2482__NODE_951_length_57243_cov_4.621488 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586256 sample name Hadza_MoBio_hadza-I-L_K_7_2482__NODE_951_length_57243_cov_4.621488 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_provirus.7 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139518 SAMEA13537548 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738180. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537548 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 27.9533 MAG coverage software Reads (ERR7738180) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 346 Submitter Id Hadza_MoBio_hadza-A-D_H_17_1555__NODE_397_length_53457_cov_16.636905_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585809 sample name Hadza_MoBio_hadza-A-D_H_17_1555__NODE_397_length_53457_cov_16.636905_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.1326 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139520 SAMEA13537550 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738180. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537550 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 55.2667 MAG coverage software Reads (ERR7738180) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 238 Submitter Id Hadza_MoBio_hadza-A-D_H_17_1555__NODE_150_length_89064_cov_32.490791 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585809 sample name Hadza_MoBio_hadza-A-D_H_17_1555__NODE_150_length_89064_cov_32.490791 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738174_virus.335 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139521 SAMEA13537551 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738180. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537551 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 12.3308 MAG coverage software Reads (ERR7738180) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_H_17_1555__NODE_258_length_67681_cov_7.310588 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.5227272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585809 sample name Hadza_MoBio_hadza-A-D_H_17_1555__NODE_258_length_67681_cov_7.310588 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380017 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139522 SAMEA13537552 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738180. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537552 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 13.1421 MAG coverage software Reads (ERR7738180) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_H_17_1555__NODE_523_length_44879_cov_7.681845 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585809 sample name Hadza_MoBio_hadza-A-D_H_17_1555__NODE_523_length_44879_cov_7.681845 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1491;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738180_virus.523 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139523 SAMEA13537553 340016 uncultured virus This sample represents an uncultured Inovirus sp. virus assembled from ERR7738180. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537553 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 8.24855 MAG coverage software Reads (ERR7738180) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_H_17_1555__NODE_6284_length_6374_cov_5.051929 Viral contig found in MAG ERR7738180_bin.29 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585809 sample name Hadza_MoBio_hadza-A-D_H_17_1555__NODE_6284_length_6374_cov_5.051929 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738180_virus.6284 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae; Inovirus; unclassified Inovirus; Inovirus sp. virus enrichment approach none ERS11139524 SAMEA13537554 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738180. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537554 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 68.8559 MAG coverage software Reads (ERR7738180) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_H_17_1555__NODE_922_length_31034_cov_45.174920 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585809 sample name Hadza_MoBio_hadza-A-D_H_17_1555__NODE_922_length_31034_cov_45.174920 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_provirus.563 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139526 SAMEA13537556 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738181. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537556 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 17.987 MAG coverage software Reads (ERR7738181) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559867) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_K_11_2484__NODE_1013_length_40891_cov_10.213064 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586258 sample name Hadza_MoBio_hadza-I-L_K_11_2484__NODE_1013_length_40891_cov_10.213064 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_virus.1013 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139527 SAMEA13537557 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738181. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537557 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 7.41338 MAG coverage software Reads (ERR7738181) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559867) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 561 Submitter Id Hadza_MoBio_hadza-I-L_K_11_2484__NODE_1257_length_35887_cov_4.094387 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586258 sample name Hadza_MoBio_hadza-I-L_K_11_2484__NODE_1257_length_35887_cov_4.094387 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.2223 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139528 SAMEA13537558 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738181. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537558 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 14.2544 MAG coverage software Reads (ERR7738181) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559867) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_K_11_2484__NODE_1893_length_27075_cov_8.124120 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586258 sample name Hadza_MoBio_hadza-I-L_K_11_2484__NODE_1893_length_27075_cov_8.124120 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_virus.1893 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139529 SAMEA13537559 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738181. BACPHLIP temperate score 0.01076461450908247 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537559 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 9.02635 MAG coverage software Reads (ERR7738181) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559867) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_K_11_2484__NODE_5637_length_11460_cov_5.106738 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586258 sample name Hadza_MoBio_hadza-I-L_K_11_2484__NODE_5637_length_11460_cov_5.106738 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257123 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900547315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_virus.5637 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139530 SAMEA13537560 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738181. BACPHLIP temperate score 0.07897769092469892 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537560 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 29.2663 MAG coverage software Reads (ERR7738181) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559867) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_K_11_2484__NODE_8359_length_8121_cov_17.038662 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586258 sample name Hadza_MoBio_hadza-I-L_K_11_2484__NODE_8359_length_8121_cov_17.038662 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_virus.8359 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139531 SAMEA13537561 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738182. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537561 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 31.124 MAG coverage software Reads (ERR7738182) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559464) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_D_3_2666__NODE_189_length_124640_cov_17.775070_1 Viral contig found in MAG ERR7738182_bin.71 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586364 sample name Hadza_MoBio_hadza-I-L_D_3_2666__NODE_189_length_124640_cov_17.775070_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747083_bin.116 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1994;s__UMGS1994 sp900556975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139532 SAMEA13537562 2133760 Siphoviridae environmental samples This sample represents an uncultured Cellulophaga phage Ingeline_8 provirus assembled from ERR7738182. BACPHLIP temperate score 0.06701541850220269 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537562 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 18.163 MAG coverage software Reads (ERR7738182) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559464) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-I-L_D_3_2666__NODE_515_length_69025_cov_10.522843_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586364 sample name Hadza_MoBio_hadza-I-L_D_3_2666__NODE_515_length_69025_cov_10.522843_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cellulophaga phage Ingeline_8 virus enrichment approach none ERS11139534 SAMEA13537564 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738182. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537564 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 10.6952 MAG coverage software Reads (ERR7738182) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559464) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 275 Submitter Id Hadza_MoBio_hadza-I-L_D_3_2666__NODE_1471_length_33310_cov_5.998255 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586364 sample name Hadza_MoBio_hadza-I-L_D_3_2666__NODE_1471_length_33310_cov_5.998255 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737969_virus.1402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139535 SAMEA13537565 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738182. BACPHLIP temperate score 0.06194933920704848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537565 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 235.35 MAG coverage software Reads (ERR7738182) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559464) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-I-L_D_3_2666__NODE_3317_length_15493_cov_135.791651 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586364 sample name Hadza_MoBio_hadza-I-L_D_3_2666__NODE_3317_length_15493_cov_135.791651 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.9369 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139536 SAMEA13537566 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738182. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537566 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 113.35 MAG coverage software Reads (ERR7738182) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559464) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_MoBio_hadza-I-L_D_3_2666__NODE_940_length_46840_cov_65.840151 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586364 sample name Hadza_MoBio_hadza-I-L_D_3_2666__NODE_940_length_46840_cov_65.840151 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_virus.471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139537 SAMEA13537567 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738183. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537567 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 2717.63 MAG coverage software Reads (ERR7738183) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560497) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_O_24_1936__NODE_156_length_38032_cov_1614.112212 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9130434782608696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586077 sample name Hadza_MoBio_hadza-E-H_O_24_1936__NODE_156_length_38032_cov_1614.112212 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737955_virus.338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139538 SAMEA13537568 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738183. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537568 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 37.3374 MAG coverage software Reads (ERR7738183) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560497) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-E-H_O_24_1936__NODE_356_length_18685_cov_22.281384 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586077 sample name Hadza_MoBio_hadza-E-H_O_24_1936__NODE_356_length_18685_cov_22.281384 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095938 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738183_virus.356 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139540 SAMEA13537570 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738184. BACPHLIP temperate score 0.06798872201629169 ENA-FIRST-PUBLIC 2022-12-27T00:30:08Z ENA-LAST-UPDATE 2022-12-27T00:30:08Z External Id SAMEA13537570 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 23.9841 MAG coverage software Reads (ERR7738184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561120) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 587 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-A-D_B_7_1597__NODE_71_length_101110_cov_13.355735_1 Viral contig found in MAG ERR7738184_bin.117 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585846 sample name Hadza_MoBio_hadza-A-D_B_7_1597__NODE_71_length_101110_cov_13.355735_1 scientific_name uncultured Caudovirales phage sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME108259 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900313215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_provirus.763 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales ERS11139541 SAMEA13537571 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738184. BACPHLIP temperate score 0.06029648506968258 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537571 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 7.65817 MAG coverage software Reads (ERR7738184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561120) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-A-D_B_7_1597__NODE_1171_length_26429_cov_4.524021 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585846 sample name Hadza_MoBio_hadza-A-D_B_7_1597__NODE_1171_length_26429_cov_4.524021 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.345 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;s__Anaerobutyricum hallii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_virus.1171 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139542 SAMEA13537572 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738184. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537572 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 30.4576 MAG coverage software Reads (ERR7738184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561120) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 311 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_B_7_1597__NODE_288_length_55023_cov_16.146180 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8867924528301887 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585846 sample name Hadza_MoBio_hadza-A-D_B_7_1597__NODE_288_length_55023_cov_16.146180 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_virus.288 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139543 SAMEA13537573 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738184. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537573 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 28.2671 MAG coverage software Reads (ERR7738184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561120) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_B_7_1597__NODE_439_length_46121_cov_15.904591 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585846 sample name Hadza_MoBio_hadza-A-D_B_7_1597__NODE_439_length_46121_cov_15.904591 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_virus.800 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139544 SAMEA13537574 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738184. BACPHLIP temperate score 0.7093893088856106 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537574 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 12.1725 MAG coverage software Reads (ERR7738184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561120) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 162 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-A-D_B_7_1597__NODE_816_length_33308_cov_6.571906 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3636363636363637 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585846 sample name Hadza_MoBio_hadza-A-D_B_7_1597__NODE_816_length_33308_cov_6.571906 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_virus.816 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139545 SAMEA13537575 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738185. BACPHLIP temperate score 0.5751674891193073 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537575 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 85.275 MAG coverage software Reads (ERR7738185) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559765) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-I-L_P_16_2361__NODE_1256_length_37297_cov_49.732348_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586228 sample name Hadza_MoBio_hadza-I-L_P_16_2361__NODE_1256_length_37297_cov_49.732348_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745427_provirus.1148 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139546 SAMEA13537576 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738185. BACPHLIP temperate score 0.00247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537576 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 58.0948 MAG coverage software Reads (ERR7738185) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559765) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_P_16_2361__NODE_669_length_58838_cov_37.217032_1 Viral contig found in MAG ERR7738185_bin.168 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586228 sample name Hadza_MoBio_hadza-I-L_P_16_2361__NODE_669_length_58838_cov_37.217032_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745403_provirus.913 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11139547 SAMEA13537577 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738185. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537577 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 15.7887 MAG coverage software Reads (ERR7738185) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559765) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 165 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-I-L_P_16_2361__NODE_1254_length_37325_cov_9.210025 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586228 sample name Hadza_MoBio_hadza-I-L_P_16_2361__NODE_1254_length_37325_cov_9.210025 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745975_bin.137 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;s__CAG-488 sp000434055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_virus.1320 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139549 SAMEA13537579 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738185. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537579 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 82.29 MAG coverage software Reads (ERR7738185) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559765) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_P_16_2361__NODE_714_length_55901_cov_46.213528 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586228 sample name Hadza_MoBio_hadza-I-L_P_16_2361__NODE_714_length_55901_cov_46.213528 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745438_bin.61 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp004553545 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745412_virus.659 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139550 SAMEA13537580 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738186. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537580 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 46.3417 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 90 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_316_length_93449_cov_27.362775_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_316_length_93449_cov_27.362775_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.557 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139551 SAMEA13537581 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus provirus assembled from ERR7738186. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537581 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 81.785 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 621 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_543_length_69216_cov_48.597680_1 Viral contig found in MAG ERR7738186_bin.64 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_543_length_69216_cov_48.597680_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738186_provirus.543 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11139552 SAMEA13537582 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738186. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537582 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 10.0364 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_1045_length_46943_cov_5.722613 Viral contig found in MAG ERR7738186_bin.58 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_1045_length_46943_cov_5.722613 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139553 SAMEA13537583 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 virus assembled from ERR7738186. BACPHLIP temperate score 0.4629947229551451 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537583 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 8.75099 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 168 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_1263_length_41699_cov_4.805512 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_1263_length_41699_cov_4.805512 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0280262 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11139555 SAMEA13537585 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738186. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537585 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 29.9326 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_233_length_107321_cov_18.046968 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_233_length_107321_cov_18.046968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738186_virus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11139556 SAMEA13537586 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738186. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537586 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 75.824700000000007 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 129 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_323_length_92481_cov_43.427709 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6176470588235294 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_323_length_92481_cov_43.427709 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.284 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139557 SAMEA13537587 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738186. BACPHLIP temperate score 0.05443336174904671 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537587 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 19.4473 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_5495_length_13343_cov_11.375320 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_5495_length_13343_cov_11.375320 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738186_virus.5495 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139558 SAMEA13537588 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738186. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537588 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 788.712 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_688_length_61468_cov_454.200762 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_688_length_61468_cov_454.200762 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746436_virus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139559 SAMEA13537589 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738186. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537589 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 76.5799 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 325 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_964_length_49517_cov_44.033981 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.45 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_964_length_49517_cov_44.033981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738192_bin.234 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp900543455 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.897 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139560 SAMEA13537590 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738187. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537590 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 17.5669 MAG coverage software Reads (ERR7738187) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_MoBio_hadza-A-D_P_11_1507__NODE_645_length_47607_cov_10.240900_1 Viral contig found in MAG ERR7738187_bin.82 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585763 sample name Hadza_MoBio_hadza-A-D_P_11_1507__NODE_645_length_47607_cov_10.240900_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746345_bin.167 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-460;s__CAG-460 sp000437315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_provirus.645 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139561 SAMEA13537591 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738187. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537591 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 21.4416 MAG coverage software Reads (ERR7738187) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-A-D_P_11_1507__NODE_1354_length_26974_cov_12.568762 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585763 sample name Hadza_MoBio_hadza-A-D_P_11_1507__NODE_1354_length_26974_cov_12.568762 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737953_virus.342 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139563 SAMEA13537593 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738187. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537593 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 11.5581 MAG coverage software Reads (ERR7738187) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_P_11_1507__NODE_754_length_42484_cov_6.258165 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585763 sample name Hadza_MoBio_hadza-A-D_P_11_1507__NODE_754_length_42484_cov_6.258165 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_virus.754 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139564 SAMEA13537594 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738188. BACPHLIP temperate score 0.05743392070484582 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537594 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 25.1872 MAG coverage software Reads (ERR7738188) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562249) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_C-REDO_A_9_1509__NODE_177_length_117489_cov_14.129655_1 Viral contig found in MAG ERR7738188_bin.75 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585765 sample name Hadza_MoBio_C-REDO_A_9_1509__NODE_177_length_117489_cov_14.129655_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747426_bin.316 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D succinifaciens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_provirus.212 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139565 SAMEA13537595 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn provirus assembled from ERR7738188. BACPHLIP temperate score 0.02113157861825958 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537595 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 15.6577 MAG coverage software Reads (ERR7738188) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562249) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 330 Number of CRISPR spacer hits supporting host taxonomy 518 Submitter Id Hadza_MoBio_C-REDO_A_9_1509__NODE_593_length_54164_cov_8.672472_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4827586206896552 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585765 sample name Hadza_MoBio_C-REDO_A_9_1509__NODE_593_length_54164_cov_8.672472_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_provirus.43 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11139566 SAMEA13537596 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738188. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537596 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 25.0623 MAG coverage software Reads (ERR7738188) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562249) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 81 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_C-REDO_A_9_1509__NODE_1309_length_30294_cov_14.328524 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585765 sample name Hadza_MoBio_C-REDO_A_9_1509__NODE_1309_length_30294_cov_14.328524 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139567 SAMEA13537597 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738188. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537597 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 40.8022 MAG coverage software Reads (ERR7738188) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562249) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 200 Submitter Id Hadza_MoBio_C-REDO_A_9_1509__NODE_271_length_88905_cov_23.499302 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9583333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585765 sample name Hadza_MoBio_C-REDO_A_9_1509__NODE_271_length_88905_cov_23.499302 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_virus.269 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139569 SAMEA13537599 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738189. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537599 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 109.783 MAG coverage software Reads (ERR7738189) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_O_3_2503__NODE_22_length_248899_cov_66.452351_1 Viral contig found in MAG ERR7738189_bin.72 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586277 sample name Hadza_MoBio_hadza-I-L_O_3_2503__NODE_22_length_248899_cov_66.452351_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_virus.540 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139570 SAMEA13537600 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738189. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537600 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 10.5485 MAG coverage software Reads (ERR7738189) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_O_3_2503__NODE_1000_length_38687_cov_6.249055 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586277 sample name Hadza_MoBio_hadza-I-L_O_3_2503__NODE_1000_length_38687_cov_6.249055 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738249_provirus.651 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139571 SAMEA13537601 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738189. BACPHLIP temperate score 0.06993392070484582 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537601 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 8.41219 MAG coverage software Reads (ERR7738189) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_O_3_2503__NODE_1493_length_29168_cov_5.069712 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586277 sample name Hadza_MoBio_hadza-I-L_O_3_2503__NODE_1493_length_29168_cov_5.069712 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_provirus.121 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139572 SAMEA13537602 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738189. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537602 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 43.4122 MAG coverage software Reads (ERR7738189) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 576 Submitter Id Hadza_MoBio_hadza-I-L_O_3_2503__NODE_183_length_96319_cov_25.797417 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586277 sample name Hadza_MoBio_hadza-I-L_O_3_2503__NODE_183_length_96319_cov_25.797417 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738198_virus.99 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139573 SAMEA13537603 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738189. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537603 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 49.3167 MAG coverage software Reads (ERR7738189) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_O_3_2503__NODE_3419_length_14530_cov_29.837404 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586277 sample name Hadza_MoBio_hadza-I-L_O_3_2503__NODE_3419_length_14530_cov_29.837404 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.7067 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11139574 SAMEA13537604 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738189. BACPHLIP temperate score 0.18145698646964648 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537604 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 17.7043 MAG coverage software Reads (ERR7738189) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_O_3_2503__NODE_564_length_54832_cov_10.930819 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9761904761904762 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586277 sample name Hadza_MoBio_hadza-I-L_O_3_2503__NODE_564_length_54832_cov_10.930819 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_virus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11139575 SAMEA13537605 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738190. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537605 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 9.3423 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 118 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1161_length_42055_cov_5.168993_1 Viral contig found in MAG ERR7738190_bin.165 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1161_length_42055_cov_5.168993_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0307965 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139576 SAMEA13537606 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738190. BACPHLIP temperate score 0.45535389006526233 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537606 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 68.4981 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 198 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_676_length_58996_cov_38.455609_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_676_length_58996_cov_38.455609_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746779_virus.285 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139578 SAMEA13537608 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738190. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537608 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 39.3663 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1279_length_39433_cov_21.912313 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1279_length_39433_cov_21.912313 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738190_virus.1279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139579 SAMEA13537609 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738190. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27T00:30:11Z ENA-LAST-UPDATE 2022-12-27T00:30:11Z External Id SAMEA13537609 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 60.1443 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 98 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1715_length_32310_cov_35.819409 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1715_length_32310_cov_35.819409 scientific_name Siphoviridae environmental samples sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.105 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp900552845 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_provirus.2122 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae ERS11139580 SAMEA13537610 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738190. BACPHLIP temperate score 0.24245594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537610 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 12.4701 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_2662_length_23293_cov_6.725793 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_2662_length_23293_cov_6.725793 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.216 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139581 SAMEA13537611 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738190. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537611 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 10.1432 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_3197_length_20094_cov_5.721637 Viral contig found in MAG ERR7738190_bin.181 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_3197_length_20094_cov_5.721637 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738614_bin.3 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__HGM13634;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.2098 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139582 SAMEA13537612 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738190. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537612 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 45.4646 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2363 Number of CRISPR spacer hits supporting host taxonomy 247 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_548_length_66731_cov_26.299532 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_548_length_66731_cov_26.299532 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745603_virus.118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139584 SAMEA13537614 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738191. BACPHLIP temperate score 0.11497797356828196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537614 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 24.0491 MAG coverage software Reads (ERR7738191) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560289) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_J_2_2306__NODE_168_length_109637_cov_14.001771_1 Viral contig found in MAG ERR7738191_bin.148 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586178 sample name Hadza_MoBio_hadza-E-H_J_2_2306__NODE_168_length_109637_cov_14.001771_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738191_provirus.168 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139585 SAMEA13537615 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738191. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537615 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 56.622 MAG coverage software Reads (ERR7738191) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560289) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 88 Number of CRISPR spacer hits supporting host taxonomy 123 Submitter Id Hadza_MoBio_hadza-E-H_J_2_2306__NODE_719_length_50670_cov_35.251675_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586178 sample name Hadza_MoBio_hadza-E-H_J_2_2306__NODE_719_length_50670_cov_35.251675_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0308158 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139586 SAMEA13537616 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738191. BACPHLIP temperate score 0.06971365638766522 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537616 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 38.8056 MAG coverage software Reads (ERR7738191) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560289) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_J_2_2306__NODE_1133_length_37270_cov_22.365768 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586178 sample name Hadza_MoBio_hadza-E-H_J_2_2306__NODE_1133_length_37270_cov_22.365768 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738191_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139587 SAMEA13537617 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738191. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537617 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 7.40059 MAG coverage software Reads (ERR7738191) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560289) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_J_2_2306__NODE_584_length_57108_cov_4.166138 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586178 sample name Hadza_MoBio_hadza-E-H_J_2_2306__NODE_584_length_57108_cov_4.166138 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128517 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900290275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.835 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139588 SAMEA13537618 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738191. BACPHLIP temperate score 0.6875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537618 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 32.5615 MAG coverage software Reads (ERR7738191) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560289) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 858 Submitter Id Hadza_MoBio_hadza-E-H_J_2_2306__NODE_947_length_42366_cov_19.049091 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586178 sample name Hadza_MoBio_hadza-E-H_J_2_2306__NODE_947_length_42366_cov_19.049091 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.235 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11139589 SAMEA13537619 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738192. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537619 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 27.7423 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 97 Number of CRISPR spacer hits supporting host taxonomy 234 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_184_length_153339_cov_15.970260_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9210526315789472 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_184_length_153339_cov_15.970260_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_provirus.591 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139590 SAMEA13537620 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738192. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537620 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 34.8521 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_68_length_239511_cov_20.132291_1 Viral contig found in MAG ERR7738192_bin.182 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_68_length_239511_cov_20.132291_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME255709 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1883;f__UMGS1883;g__UMGS1540;s__UMGS1540 sp900552775 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738192_provirus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139592 SAMEA13537622 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738192. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537622 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 25.2144 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_1381_length_44149_cov_15.200309 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_1381_length_44149_cov_15.200309 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.224 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__Ruminococcus sp900540005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.1072 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139593 SAMEA13537623 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738192. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537623 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 25.6317 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_1748_length_36407_cov_15.098541 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_1748_length_36407_cov_15.098541 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.734 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139594 SAMEA13537624 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738192. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537624 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 163.232 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_2262_length_29662_cov_95.089032 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_2262_length_29662_cov_95.089032 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME029635 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417;s__CAG-417 sp000432835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.1296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139595 SAMEA13537625 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738192. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537625 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 10.0316 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_3378_length_20509_cov_5.772661 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_3378_length_20509_cov_5.772661 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738192_virus.3378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11139596 SAMEA13537626 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738192. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537626 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 9.67269 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_712_length_69814_cov_5.467800 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_712_length_69814_cov_5.467800 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738651_bin.237 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA5905;s__UBA5905 sp900763035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139598 SAMEA13537628 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738193. BACPHLIP temperate score 0.11976362772252648 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537628 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 11.5775 MAG coverage software Reads (ERR7738193) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561932) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-I-L_F_3_2652__NODE_740_length_48954_cov_7.204350_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106183 sample name Hadza_MoBio_hadza-I-L_F_3_2652__NODE_740_length_48954_cov_7.204350_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139599 SAMEA13537629 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738193. BACPHLIP temperate score 0.03997797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537629 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 20.1376 MAG coverage software Reads (ERR7738193) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561932) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_F_3_2652__NODE_1489_length_29840_cov_12.041058 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106183 sample name Hadza_MoBio_hadza-I-L_F_3_2652__NODE_1489_length_29840_cov_12.041058 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738216_bin.19 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp900555115 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.1720 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139600 SAMEA13537630 2100421 uncultured Caudovirales phage This sample represents an uncultured Beecentumtrevirus virus assembled from ERR7738193. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537630 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 13.0951 MAG coverage software Reads (ERR7738193) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561932) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_F_3_2652__NODE_3087_length_16382_cov_8.079301 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106183 sample name Hadza_MoBio_hadza-I-L_F_3_2652__NODE_3087_length_16382_cov_8.079301 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738569_virus.5962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae; Picovirinae; Beecentumtrevirus virus enrichment approach none ERS11139601 SAMEA13537631 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738193. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537631 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 72.1019 MAG coverage software Reads (ERR7738193) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561932) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 224 Submitter Id Hadza_MoBio_hadza-I-L_F_3_2652__NODE_518_length_61914_cov_44.522228 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.35294117647058826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106183 sample name Hadza_MoBio_hadza-I-L_F_3_2652__NODE_518_length_61914_cov_44.522228 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745603_virus.118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139602 SAMEA13537632 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738193. BACPHLIP temperate score 0.2849118942731278 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537632 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 30.2629 MAG coverage software Reads (ERR7738193) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561932) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-I-L_F_3_2652__NODE_71_length_160186_cov_18.367050 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106183 sample name Hadza_MoBio_hadza-I-L_F_3_2652__NODE_71_length_160186_cov_18.367050 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738167_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFHK01;s__SFHK01 sp004556395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.92 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139603 SAMEA13537633 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738193. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537633 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 8.30731 MAG coverage software Reads (ERR7738193) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561932) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 79 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_F_3_2652__NODE_962_length_40478_cov_4.922279 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7096774193548387 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106183 sample name Hadza_MoBio_hadza-I-L_F_3_2652__NODE_962_length_40478_cov_4.922279 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.1446 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139604 SAMEA13537634 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738194. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537634 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 37.3286 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 388 Number of CRISPR spacer hits supporting host taxonomy 135 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_400_length_79425_cov_21.787153_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_400_length_79425_cov_21.787153_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME150720 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp003526955 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_provirus.400 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139605 SAMEA13537635 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738194. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537635 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 28.9007 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 100 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_730_length_58768_cov_16.957660_1 Viral contig found in MAG ERR7738194_bin.95 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_730_length_58768_cov_16.957660_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745975_bin.137 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;s__CAG-488 sp000434055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_provirus.730 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139607 SAMEA13537637 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738194. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537637 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 14.3376 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 183 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1231_length_41819_cov_8.066096 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1231_length_41819_cov_8.066096 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.1231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139608 SAMEA13537638 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738194. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537638 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 71.7565 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1517_length_36459_cov_48.597823 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1517_length_36459_cov_48.597823 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257123 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900547315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.1517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139609 SAMEA13537639 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738194. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537639 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 58.4132 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 218 Number of CRISPR spacer hits supporting host taxonomy 101 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1706_length_33988_cov_33.323376 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1706_length_33988_cov_33.323376 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.1706 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139610 SAMEA13537640 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738194. BACPHLIP temperate score 0.04365360504997764 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537640 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 7.99427 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_2380_length_26849_cov_4.146571 Viral contig found in MAG ERR7738194_bin.222 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_2380_length_26849_cov_4.146571 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.2380 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139611 SAMEA13537641 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738194. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537641 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 8.99867 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_3953_length_18238_cov_4.983977 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_3953_length_18238_cov_4.983977 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.3953 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139613 SAMEA13537643 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738195. BACPHLIP temperate score 0.12687137493752415 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537643 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 280.018 MAG coverage software Reads (ERR7738195) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 358 Submitter Id Hadza_MoBio_C-REDO_E_9_1560__NODE_229_length_97919_cov_155.699005_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585814 sample name Hadza_MoBio_C-REDO_E_9_1560__NODE_229_length_97919_cov_155.699005_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746692_virus.1019 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139614 SAMEA13537644 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738195. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537644 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 8.2816 MAG coverage software Reads (ERR7738195) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_C-REDO_E_9_1560__NODE_1705_length_23811_cov_4.521151 Viral contig found in MAG ERR7738195_bin.70 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585814 sample name Hadza_MoBio_C-REDO_E_9_1560__NODE_1705_length_23811_cov_4.521151 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738555_provirus.57 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139615 SAMEA13537645 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738195. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537645 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 17.1864 MAG coverage software Reads (ERR7738195) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_E_9_1560__NODE_5293_length_8308_cov_9.565059 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585814 sample name Hadza_MoBio_C-REDO_E_9_1560__NODE_5293_length_8308_cov_9.565059 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745433_virus.4077 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139616 SAMEA13537646 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738195. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537646 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 10.1481 MAG coverage software Reads (ERR7738195) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 108 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_C-REDO_E_9_1560__NODE_740_length_47505_cov_5.493759 Viral contig found in MAG ERR7738195_bin.68 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6046511627906976 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585814 sample name Hadza_MoBio_C-REDO_E_9_1560__NODE_740_length_47505_cov_5.493759 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-4429795 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139617 SAMEA13537647 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738196. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537647 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 111.397 MAG coverage software Reads (ERR7738196) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559919) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_M_21_2500__NODE_17_length_248769_cov_65.440083_1 Viral contig found in MAG ERR7738196_bin.125 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586274 sample name Hadza_MoBio_hadza-I-L_M_21_2500__NODE_17_length_248769_cov_65.440083_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_virus.540 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139618 SAMEA13537648 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738196. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537648 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 73.2128 MAG coverage software Reads (ERR7738196) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559919) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_hadza-I-L_M_21_2500__NODE_1304_length_32666_cov_41.987511 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586274 sample name Hadza_MoBio_hadza-I-L_M_21_2500__NODE_1304_length_32666_cov_41.987511 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746344_bin.124 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745420_virus.880 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139619 SAMEA13537649 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738196. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537649 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 42.3546 MAG coverage software Reads (ERR7738196) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559919) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 572 Submitter Id Hadza_MoBio_hadza-I-L_M_21_2500__NODE_185_length_96319_cov_24.586397 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586274 sample name Hadza_MoBio_hadza-I-L_M_21_2500__NODE_185_length_96319_cov_24.586397 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738198_virus.99 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139621 SAMEA13537651 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738196. BACPHLIP temperate score 0.08631662166094103 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537651 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 97.5251 MAG coverage software Reads (ERR7738196) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559919) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_M_21_2500__NODE_561_length_53920_cov_59.888231 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586274 sample name Hadza_MoBio_hadza-I-L_M_21_2500__NODE_561_length_53920_cov_59.888231 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.703 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139622 SAMEA13537652 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738196. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537652 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 7.94157 MAG coverage software Reads (ERR7738196) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559919) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 279 Submitter Id Hadza_MoBio_hadza-I-L_M_21_2500__NODE_822_length_43792_cov_4.420725 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4230769230769231 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586274 sample name Hadza_MoBio_hadza-I-L_M_21_2500__NODE_822_length_43792_cov_4.420725 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127;s__CAG-127 sp900319515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738196_virus.822 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139623 SAMEA13537653 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus provirus assembled from ERR7738197. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537653 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 15.2905 MAG coverage software Reads (ERR7738197) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559597) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_B_1_2682__NODE_1362_length_42048_cov_9.764433_1 Viral contig found in MAG ERR7738197_bin.28 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586379 sample name Hadza_MoBio_hadza-I-L_B_1_2682__NODE_1362_length_42048_cov_9.764433_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_provirus.1362 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11139624 SAMEA13537654 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738197. BACPHLIP temperate score 0.07747797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537654 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 110.611 MAG coverage software Reads (ERR7738197) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559597) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-I-L_B_1_2682__NODE_489_length_80775_cov_70.747937_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586379 sample name Hadza_MoBio_hadza-I-L_B_1_2682__NODE_489_length_80775_cov_70.747937_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_virus.773 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139625 SAMEA13537655 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738197. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537655 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 120.667 MAG coverage software Reads (ERR7738197) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559597) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-I-L_B_1_2682__NODE_1319_length_42696_cov_70.770454 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586379 sample name Hadza_MoBio_hadza-I-L_B_1_2682__NODE_1319_length_42696_cov_70.770454 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.1742 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139342 SAMEA13537372 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738147. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-26 ENA-LAST-UPDATE 2022-12-26 External Id SAMEA13537372 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-26T20:28:40Z INSDC last update 2022-12-26T20:28:40Z INSDC status public MAG coverage depth 16.0522 MAG coverage software Reads (ERR7738147) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559941) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 118 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-E-H_B_21_1948__NODE_479_length_46264_cov_9.405850_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586087 sample name Hadza_MoBio_hadza-E-H_B_21_1948__NODE_479_length_46264_cov_9.405850_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0307965 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139467 SAMEA13537497 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738170. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537497 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:05Z INSDC last update 2022-12-27T00:30:05Z INSDC status public MAG coverage depth 10.5295 MAG coverage software Reads (ERR7738170) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_B_5_2673__NODE_2484_length_23415_cov_5.849216 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586371 sample name Hadza_MoBio_hadza-I-L_B_5_2673__NODE_2484_length_23415_cov_5.849216 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0296258 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139475 SAMEA13537505 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738172. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537505 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 9.48438 MAG coverage software Reads (ERR7738172) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_MoBio_hadza-I-L_D_1_2641__NODE_2361_length_22038_cov_5.301307 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586345 sample name Hadza_MoBio_hadza-I-L_D_1_2641__NODE_2361_length_22038_cov_5.301307 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738172_virus.2361 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11139481 SAMEA13537511 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738173. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537511 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 29.2109 MAG coverage software Reads (ERR7738173) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 229 Submitter Id Hadza_MoBio_hadza-I-L_B_4_1344__NODE_917_length_28298_cov_16.824563 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_B_4_1344__NODE_917_length_28298_cov_16.824563 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738246_virus.447 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139490 SAMEA13537520 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738176. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537520 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 21.0729 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_1014_length_40498_cov_12.736350 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_1014_length_40498_cov_12.736350 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_virus.1014 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139496 SAMEA13537526 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7738176. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537526 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:06Z INSDC last update 2022-12-27T00:30:06Z INSDC status public MAG coverage depth 8.2805 MAG coverage software Reads (ERR7738176) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 97 Submitter Id Hadza_MoBio_hadza-A-D_H_5_1561__NODE_8261_length_9929_cov_4.786947 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585815 sample name Hadza_MoBio_hadza-A-D_H_5_1561__NODE_8261_length_9929_cov_4.786947 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738575_bin.23 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-279;s__CAG-279 sp000437795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_provirus.1115 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11139503 SAMEA13537533 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738178. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537533 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 16.6517 MAG coverage software Reads (ERR7738178) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559934) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_M_23_2501__NODE_13_length_305394_cov_9.780061_1 Viral contig found in MAG ERR7738178_bin.62 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586275 sample name Hadza_MoBio_hadza-I-L_M_23_2501__NODE_13_length_305394_cov_9.780061_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag1;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738174_provirus.240 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139509 SAMEA13537539 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738178. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537539 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 21.149 MAG coverage software Reads (ERR7738178) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559934) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Hadza_MoBio_hadza-I-L_M_23_2501__NODE_841_length_47256_cov_12.308018 Viral contig found in MAG ERR7738178_bin.23 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586275 sample name Hadza_MoBio_hadza-I-L_M_23_2501__NODE_841_length_47256_cov_12.308018 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738178_virus.841 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139519 SAMEA13537549 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738180. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537549 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 44.1781 MAG coverage software Reads (ERR7738180) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_H_17_1555__NODE_113_length_108902_cov_26.852736 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.7714285714285715 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585809 sample name Hadza_MoBio_hadza-A-D_H_17_1555__NODE_113_length_108902_cov_26.852736 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.506 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139525 SAMEA13537555 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738181. BACPHLIP temperate score 0.5875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537555 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 198.887 MAG coverage software Reads (ERR7738181) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559867) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_K_11_2484__NODE_381_length_74804_cov_123.307707_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586258 sample name Hadza_MoBio_hadza-I-L_K_11_2484__NODE_381_length_74804_cov_123.307707_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_virus.345 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139533 SAMEA13537563 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7738182. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537563 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 50.8034 MAG coverage software Reads (ERR7738182) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559464) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_MoBio_hadza-I-L_D_3_2666__NODE_95_length_163759_cov_29.377812_1 Viral contig found in MAG ERR7738182_bin.134 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48148148148148145 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586364 sample name Hadza_MoBio_hadza-I-L_D_3_2666__NODE_95_length_163759_cov_29.377812_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.1266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11139539 SAMEA13537569 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738184. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537569 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 17.9567 MAG coverage software Reads (ERR7738184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561120) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 181 Submitter Id Hadza_MoBio_hadza-A-D_B_7_1597__NODE_22_length_148309_cov_10.625486_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 23 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585846 sample name Hadza_MoBio_hadza-A-D_B_7_1597__NODE_22_length_148309_cov_10.625486_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746785_provirus.63 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139548 SAMEA13537578 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738185. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537578 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 16.6105 MAG coverage software Reads (ERR7738185) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559765) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 135 Submitter Id Hadza_MoBio_hadza-I-L_P_16_2361__NODE_283_length_102807_cov_9.517385 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8108108108108109 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586228 sample name Hadza_MoBio_hadza-I-L_P_16_2361__NODE_283_length_102807_cov_9.517385 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME101580 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster;s__Enterocloster sp000431375 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_virus.367 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139554 SAMEA13537584 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738186. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537584 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 9.79273 MAG coverage software Reads (ERR7738186) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559485) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-I-L_B_15_2660__NODE_1545_length_36185_cov_5.694417 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586361 sample name Hadza_MoBio_hadza-I-L_B_15_2660__NODE_1545_length_36185_cov_5.694417 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.1657 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139562 SAMEA13537592 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738187. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537592 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 22.0476 MAG coverage software Reads (ERR7738187) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 220 Submitter Id Hadza_MoBio_hadza-A-D_P_11_1507__NODE_316_length_81249_cov_24.379133 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.56 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585763 sample name Hadza_MoBio_hadza-A-D_P_11_1507__NODE_316_length_81249_cov_24.379133 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_virus.316 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139568 SAMEA13537598 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738188. BACPHLIP temperate score 0.1432089863334723 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537598 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 213.016 MAG coverage software Reads (ERR7738188) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562249) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_A_9_1509__NODE_819_length_42249_cov_121.121242 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585765 sample name Hadza_MoBio_C-REDO_A_9_1509__NODE_819_length_42249_cov_121.121242 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139577 SAMEA13537607 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738190. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537607 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 47.2894 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1125_length_42738_cov_26.983381 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_1125_length_42738_cov_26.983381 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124703 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_virus.1371 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139583 SAMEA13537613 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738190. BACPHLIP temperate score 0.814977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537613 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 12.942 MAG coverage software Reads (ERR7738190) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560021) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 625 Submitter Id Hadza_MoBio_hadza-E-H_N_19_2137__NODE_785_length_53423_cov_7.109661 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586123 sample name Hadza_MoBio_hadza-E-H_N_19_2137__NODE_785_length_53423_cov_7.109661 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139591 SAMEA13537621 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738192. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537621 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 13.1053 MAG coverage software Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_O_22_1935__NODE_891_length_60040_cov_7.559378_1 Viral contig found in MAG ERR7738192_bin.160 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 64.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586076 sample name Hadza_MoBio_hadza-E-H_O_22_1935__NODE_891_length_60040_cov_7.559378_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738192_provirus.891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139597 SAMEA13537627 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738193. BACPHLIP temperate score 0.02597739359623315 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537627 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 27.936 MAG coverage software Reads (ERR7738193) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561932) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-I-L_F_3_2652__NODE_190_length_109696_cov_17.347504_1 Viral contig found in MAG ERR7738193_bin.36 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106183 sample name Hadza_MoBio_hadza-I-L_F_3_2652__NODE_190_length_109696_cov_17.347504_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257483 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__UBA644;g__UBA644;s__UBA644 sp900547165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_provirus.217 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139606 SAMEA13537636 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738194. BACPHLIP temperate score 0.1641249917049939 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537636 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 22.1604 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1059_length_46092_cov_12.644594 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9534883720930232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_1059_length_46092_cov_12.644594 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME026750 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_provirus.108 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139612 SAMEA13537642 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738194. BACPHLIP temperate score 0.16667301809413704 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537642 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 6.47565 MAG coverage software Reads (ERR7738194) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560009) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_D_1_1951__NODE_7493_length_11013_cov_3.341533 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586089 sample name Hadza_MoBio_hadza-E-H_D_1_1951__NODE_7493_length_11013_cov_3.341533 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.7493 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139620 SAMEA13537650 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738196. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537650 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 74.8585 MAG coverage software Reads (ERR7738196) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559919) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_M_21_2500__NODE_333_length_72135_cov_43.864096 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586274 sample name Hadza_MoBio_hadza-I-L_M_21_2500__NODE_333_length_72135_cov_43.864096 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139626 SAMEA13537656 1478972 Gokushovirinae environmental samples This sample represents an uncultured Gokushovirus WZ-2015a virus assembled from ERR7738197. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537656 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 27.9793 MAG coverage software Reads (ERR7738197) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559597) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_hadza-I-L_B_1_2682__NODE_17023_length_5072_cov_18.465465 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586379 sample name Hadza_MoBio_hadza-I-L_B_1_2682__NODE_17023_length_5072_cov_18.465465 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_provirus.14699 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; unclassified Gokushovirinae; Gokushovirus WZ-2015a virus enrichment approach none ERS11139627 SAMEA13537657 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738197. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537657 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 5.84221 MAG coverage software Reads (ERR7738197) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559597) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_B_1_2682__NODE_29687_length_3192_cov_3.334831 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586379 sample name Hadza_MoBio_hadza-I-L_B_1_2682__NODE_29687_length_3192_cov_3.334831 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_virus.29687 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11139628 SAMEA13537658 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738197. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537658 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 81.9448 MAG coverage software Reads (ERR7738197) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559597) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_B_1_2682__NODE_480_length_81486_cov_48.617929 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6451612903225806 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586379 sample name Hadza_MoBio_hadza-I-L_B_1_2682__NODE_480_length_81486_cov_48.617929 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.856 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139629 SAMEA13537659 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738197. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537659 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 19.3755 MAG coverage software Reads (ERR7738197) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559597) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3190 Submitter Id Hadza_MoBio_hadza-I-L_B_1_2682__NODE_950_length_53984_cov_12.165674 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586379 sample name Hadza_MoBio_hadza-I-L_B_1_2682__NODE_950_length_53984_cov_12.165674 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_virus.950 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139630 SAMEA13537660 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738198. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537660 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 10.3521 MAG coverage software Reads (ERR7738198) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561738) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_J_23_1260__NODE_900_length_32401_cov_6.039723_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585678 sample name Hadza_MoBio_hadza-I-L_J_23_1260__NODE_900_length_32401_cov_6.039723_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738198_provirus.900 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139631 SAMEA13537661 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738198. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537661 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 63.5491 MAG coverage software Reads (ERR7738198) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561738) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-I-L_J_23_1260__NODE_157_length_81288_cov_36.792417 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585678 sample name Hadza_MoBio_hadza-I-L_J_23_1260__NODE_157_length_81288_cov_36.792417 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738198_virus.157 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139632 SAMEA13537662 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738198. BACPHLIP temperate score 0.07320867667127609 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537662 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 11.0437 MAG coverage software Reads (ERR7738198) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561738) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_J_23_1260__NODE_38_length_151525_cov_6.267848 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585678 sample name Hadza_MoBio_hadza-I-L_J_23_1260__NODE_38_length_151525_cov_6.267848 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME260425 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492;s__CAG-492 sp000434335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.187 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139633 SAMEA13537663 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738198. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537663 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 21.2321 MAG coverage software Reads (ERR7738198) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561738) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_MoBio_hadza-I-L_J_23_1260__NODE_54_length_134137_cov_12.501775 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.6101694915254238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585678 sample name Hadza_MoBio_hadza-I-L_J_23_1260__NODE_54_length_134137_cov_12.501775 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.70 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139634 SAMEA13537664 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738198. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537664 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 7.76566 MAG coverage software Reads (ERR7738198) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561738) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_J_23_1260__NODE_855_length_33558_cov_4.349183 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585678 sample name Hadza_MoBio_hadza-I-L_J_23_1260__NODE_855_length_33558_cov_4.349183 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.828 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139635 SAMEA13537665 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738199. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537665 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 37.1876 MAG coverage software Reads (ERR7738199) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-A-D_J_9_1548__NODE_453_length_48892_cov_22.764396_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585802 sample name Hadza_MoBio_hadza-A-D_J_9_1548__NODE_453_length_48892_cov_22.764396_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_provirus.507 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139636 SAMEA13537666 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738199. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537666 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 22.6965 MAG coverage software Reads (ERR7738199) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 165 Submitter Id Hadza_MoBio_hadza-A-D_J_9_1548__NODE_112_length_97209_cov_13.256373 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.2962962962962963 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585802 sample name Hadza_MoBio_hadza-A-D_J_9_1548__NODE_112_length_97209_cov_13.256373 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738199_virus.112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139637 SAMEA13537667 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738199. BACPHLIP temperate score 0.02747797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537667 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 52.6756 MAG coverage software Reads (ERR7738199) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-A-D_J_9_1548__NODE_264_length_65253_cov_32.292424 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585802 sample name Hadza_MoBio_hadza-A-D_J_9_1548__NODE_264_length_65253_cov_32.292424 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745874_virus.174 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139638 SAMEA13537668 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738199. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537668 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 8.97805 MAG coverage software Reads (ERR7738199) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560895) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-A-D_J_9_1548__NODE_544_length_44120_cov_5.181232 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585802 sample name Hadza_MoBio_hadza-A-D_J_9_1548__NODE_544_length_44120_cov_5.181232 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745967_virus.496 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139639 SAMEA13537669 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738200. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537669 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 28.0176 MAG coverage software Reads (ERR7738200) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560555) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 233 Submitter Id Hadza_MoBio_hadza-A-D_F_22_1638__NODE_1_length_507761_cov_17.099950_1 Viral contig found in MAG ERR7738200_bin.35 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585882 sample name Hadza_MoBio_hadza-A-D_F_22_1638__NODE_1_length_507761_cov_17.099950_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738256_provirus.224 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139640 SAMEA13537670 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738200. BACPHLIP temperate score 0.575 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537670 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 70.7952 MAG coverage software Reads (ERR7738200) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560555) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 252 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_F_22_1638__NODE_275_length_82794_cov_42.424302_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585882 sample name Hadza_MoBio_hadza-A-D_F_22_1638__NODE_275_length_82794_cov_42.424302_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.160 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139641 SAMEA13537671 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738200. BACPHLIP temperate score 0.05721365638766521 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537671 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 42.2316 MAG coverage software Reads (ERR7738200) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560555) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 186 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_F_22_1638__NODE_654_length_52794_cov_26.946184_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585882 sample name Hadza_MoBio_hadza-A-D_F_22_1638__NODE_654_length_52794_cov_26.946184_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.1137 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139642 SAMEA13537672 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738200. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537672 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 94.371 MAG coverage software Reads (ERR7738200) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560555) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 627 Number of CRISPR spacer hits supporting host taxonomy 328 Submitter Id Hadza_MoBio_hadza-A-D_F_22_1638__NODE_1306_length_35321_cov_58.344342 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585882 sample name Hadza_MoBio_hadza-A-D_F_22_1638__NODE_1306_length_35321_cov_58.344342 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738534_virus.1616 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139643 SAMEA13537673 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738200. BACPHLIP temperate score 0.15495594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537673 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 12.5295 MAG coverage software Reads (ERR7738200) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560555) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_hadza-A-D_F_22_1638__NODE_2177_length_25131_cov_7.647282 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585882 sample name Hadza_MoBio_hadza-A-D_F_22_1638__NODE_2177_length_25131_cov_7.647282 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.2254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139644 SAMEA13537674 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738200. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537674 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 9.28698 MAG coverage software Reads (ERR7738200) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560555) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-A-D_F_22_1638__NODE_637_length_53544_cov_5.574654 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585882 sample name Hadza_MoBio_hadza-A-D_F_22_1638__NODE_637_length_53544_cov_5.574654 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.506 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11139645 SAMEA13537675 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7738201. BACPHLIP temperate score 0.4875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537675 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 858.972 MAG coverage software Reads (ERR7738201) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559521) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_D_21_2679__NODE_105_length_169732_cov_503.747594_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8955223880597015 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586377 sample name Hadza_MoBio_hadza-I-L_D_21_2679__NODE_105_length_169732_cov_503.747594_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_virus.260 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139646 SAMEA13537676 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738201. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537676 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 22.2824 MAG coverage software Reads (ERR7738201) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559521) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-I-L_D_21_2679__NODE_371_length_78379_cov_13.525491_1 Viral contig found in MAG ERR7738201_bin.85 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586377 sample name Hadza_MoBio_hadza-I-L_D_21_2679__NODE_371_length_78379_cov_13.525491_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095983 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;s__Mediterraneibacter lactaris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737968_provirus.496 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139647 SAMEA13537677 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738201. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537677 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 17.0116 MAG coverage software Reads (ERR7738201) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559521) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-I-L_D_21_2679__NODE_177_length_125803_cov_9.728656 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586377 sample name Hadza_MoBio_hadza-I-L_D_21_2679__NODE_177_length_125803_cov_9.728656 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745888_virus.65 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139648 SAMEA13537678 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738201. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537678 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 43.5178 MAG coverage software Reads (ERR7738201) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559521) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 486 Number of CRISPR spacer hits supporting host taxonomy 1928 Submitter Id Hadza_MoBio_hadza-I-L_D_21_2679__NODE_841_length_39070_cov_25.505450 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6774193548387096 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586377 sample name Hadza_MoBio_hadza-I-L_D_21_2679__NODE_841_length_39070_cov_25.505450 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0339015 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139649 SAMEA13537679 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738202. BACPHLIP temperate score 0.6 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537679 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 37.6967 MAG coverage software Reads (ERR7738202) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560964) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 880 Submitter Id Hadza_MoBio_C-REDO_E_5_1556__NODE_368_length_48947_cov_16.269634_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_MoBio_C-REDO_E_5_1556__NODE_368_length_48947_cov_16.269634_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.235 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11139650 SAMEA13537680 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738202. BACPHLIP temperate score 0.18368843659633977 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537680 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 13.0636 MAG coverage software Reads (ERR7738202) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560964) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 128 Number of CRISPR spacer hits supporting host taxonomy 374 Submitter Id Hadza_MoBio_C-REDO_E_5_1556__NODE_1161_length_23298_cov_5.923819 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_MoBio_C-REDO_E_5_1556__NODE_1161_length_23298_cov_5.923819 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11139651 SAMEA13537681 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738202. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537681 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 15.8751 MAG coverage software Reads (ERR7738202) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560964) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_C-REDO_E_5_1556__NODE_338_length_51319_cov_7.973186 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_MoBio_C-REDO_E_5_1556__NODE_338_length_51319_cov_7.973186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025308 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738202_virus.338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139652 SAMEA13537682 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738202. BACPHLIP temperate score 0.22488986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537682 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 108.68 MAG coverage software Reads (ERR7738202) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560964) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_C-REDO_E_5_1556__NODE_697_length_32456_cov_48.300133 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_MoBio_C-REDO_E_5_1556__NODE_697_length_32456_cov_48.300133 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746233_virus.358 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139653 SAMEA13537683 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738203. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537683 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 126.749 MAG coverage software Reads (ERR7738203) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560247) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 970 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-E-H_H_12_2277__NODE_343_length_78247_cov_75.449648_1 Viral contig found in MAG ERR7738203_bin.82 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_MoBio_hadza-E-H_H_12_2277__NODE_343_length_78247_cov_75.449648_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_provirus.343 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11139654 SAMEA13537684 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738203. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537684 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 118.494 MAG coverage software Reads (ERR7738203) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560247) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_H_12_2277__NODE_1098_length_38386_cov_69.585476 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_MoBio_hadza-E-H_H_12_2277__NODE_1098_length_38386_cov_69.585476 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.1126 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139655 SAMEA13537685 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738203. BACPHLIP temperate score 0.08777445863796453 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537685 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 18.8816 MAG coverage software Reads (ERR7738203) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560247) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_H_12_2277__NODE_196_length_105495_cov_10.505777 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.972972972972973 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_MoBio_hadza-E-H_H_12_2277__NODE_196_length_105495_cov_10.505777 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11139656 SAMEA13537686 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738203. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537686 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 53.5489 MAG coverage software Reads (ERR7738203) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560247) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_H_12_2277__NODE_4002_length_14106_cov_30.864345 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_MoBio_hadza-E-H_H_12_2277__NODE_4002_length_14106_cov_30.864345 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000493 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea;s__Dorea formicigenerans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.4002 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139657 SAMEA13537687 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738203. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537687 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 107.697 MAG coverage software Reads (ERR7738203) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560247) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 221 Submitter Id Hadza_MoBio_hadza-E-H_H_12_2277__NODE_645_length_53837_cov_62.035342 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_MoBio_hadza-E-H_H_12_2277__NODE_645_length_53837_cov_62.035342 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.645 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11139658 SAMEA13537688 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738204. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537688 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 13.0705 MAG coverage software Reads (ERR7738204) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560453) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 104 Submitter Id Hadza_MoBio_hadza-E-H_E_6_1848__NODE_169_length_85678_cov_7.832782_1 Viral contig found in MAG ERR7738204_bin.130 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586033 sample name Hadza_MoBio_hadza-E-H_E_6_1848__NODE_169_length_85678_cov_7.832782_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738260_provirus.151 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139659 SAMEA13537689 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738204. BACPHLIP temperate score 0.0213092263283177 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537689 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 19.1333 MAG coverage software Reads (ERR7738204) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560453) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_E_6_1848__NODE_62_length_123979_cov_10.712797_1 Viral contig found in MAG ERR7738204_bin.8 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586033 sample name Hadza_MoBio_hadza-E-H_E_6_1848__NODE_62_length_123979_cov_10.712797_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_provirus.230 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139660 SAMEA13537690 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738204. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537690 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 12.9649 MAG coverage software Reads (ERR7738204) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560453) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 277 Submitter Id Hadza_MoBio_hadza-E-H_E_6_1848__NODE_131_length_96442_cov_7.828413 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.34615384615384615 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586033 sample name Hadza_MoBio_hadza-E-H_E_6_1848__NODE_131_length_96442_cov_7.828413 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738204_virus.131 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139661 SAMEA13537691 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738204. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537691 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 67.1591 MAG coverage software Reads (ERR7738204) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560453) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 243 Submitter Id Hadza_MoBio_hadza-E-H_E_6_1848__NODE_338_length_62662_cov_40.258528 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586033 sample name Hadza_MoBio_hadza-E-H_E_6_1848__NODE_338_length_62662_cov_40.258528 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738182_virus.387 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139662 SAMEA13537692 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738204. BACPHLIP temperate score 0.01328965839962564 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537692 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 10.9481 MAG coverage software Reads (ERR7738204) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560453) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_E_6_1848__NODE_59_length_125014_cov_6.093967 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586033 sample name Hadza_MoBio_hadza-E-H_E_6_1848__NODE_59_length_125014_cov_6.093967 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.143 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139663 SAMEA13537693 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738205. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537693 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 31.1773 MAG coverage software Reads (ERR7738205) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_L_21_1526__NODE_1655_length_24804_cov_17.572330_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_MoBio_hadza-A-D_L_21_1526__NODE_1655_length_24804_cov_17.572330_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_virus.1581 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139664 SAMEA13537694 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738205. BACPHLIP temperate score 0.130873179909068 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537694 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 15.8022 MAG coverage software Reads (ERR7738205) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 107 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_L_21_1526__NODE_597_length_53170_cov_8.982766_1 Viral contig found in MAG ERR7738205_bin.26 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_MoBio_hadza-A-D_L_21_1526__NODE_597_length_53170_cov_8.982766_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.1123 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139665 SAMEA13537695 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738205. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537695 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 14.129 MAG coverage software Reads (ERR7738205) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_L_21_1526__NODE_1333_length_29297_cov_8.035592 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9642857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_MoBio_hadza-A-D_L_21_1526__NODE_1333_length_29297_cov_8.035592 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738205_virus.1333 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139666 SAMEA13537696 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr273_1 virus assembled from ERR7738205. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537696 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 25.9267 MAG coverage software Reads (ERR7738205) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_L_21_1526__NODE_230_length_96459_cov_15.048764 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7913043478260869 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_MoBio_hadza-A-D_L_21_1526__NODE_230_length_96459_cov_15.048764 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746111_bin.22 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.332 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr273_1 virus enrichment approach none ERS11139667 SAMEA13537697 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738205. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537697 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 30.4653 MAG coverage software Reads (ERR7738205) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 516 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_L_21_1526__NODE_472_length_63806_cov_18.677682 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_MoBio_hadza-A-D_L_21_1526__NODE_472_length_63806_cov_18.677682 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139668 SAMEA13537698 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738205. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537698 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 13.1344 MAG coverage software Reads (ERR7738205) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562320) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 402 Submitter Id Hadza_MoBio_hadza-A-D_L_21_1526__NODE_836_length_41138_cov_7.564307 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7407407407407407 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_MoBio_hadza-A-D_L_21_1526__NODE_836_length_41138_cov_7.564307 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME176098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.2049 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139669 SAMEA13537699 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738206. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537699 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 15.0475 MAG coverage software Reads (ERR7738206) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_P_20_2353__NODE_204_length_93947_cov_8.719335_1 Viral contig found in MAG ERR7738206_bin.48 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.903846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586220 sample name Hadza_MoBio_hadza-E-H_P_20_2353__NODE_204_length_93947_cov_8.719335_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.1234 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11139670 SAMEA13537700 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738206. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537700 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 83.9444 MAG coverage software Reads (ERR7738206) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_P_20_2353__NODE_693_length_47709_cov_49.455492_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586220 sample name Hadza_MoBio_hadza-E-H_P_20_2353__NODE_693_length_47709_cov_49.455492_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_provirus.420 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139671 SAMEA13537701 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738206. BACPHLIP temperate score 0.10914096916299568 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537701 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 9.3297 MAG coverage software Reads (ERR7738206) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 268 Submitter Id Hadza_MoBio_hadza-E-H_P_20_2353__NODE_1198_length_33826_cov_5.385789 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586220 sample name Hadza_MoBio_hadza-E-H_P_20_2353__NODE_1198_length_33826_cov_5.385789 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0331948 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139672 SAMEA13537702 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738206. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537702 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 12.8131 MAG coverage software Reads (ERR7738206) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 459 Submitter Id Hadza_MoBio_hadza-E-H_P_20_2353__NODE_167_length_100528_cov_7.511294 Viral contig found in MAG ERR7738206_bin.13 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5671641791044776 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586220 sample name Hadza_MoBio_hadza-E-H_P_20_2353__NODE_167_length_100528_cov_7.511294 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_virus.236 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139673 SAMEA13537703 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738206. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537703 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 168.689 MAG coverage software Reads (ERR7738206) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Hadza_MoBio_hadza-E-H_P_20_2353__NODE_543_length_55561_cov_110.091342 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586220 sample name Hadza_MoBio_hadza-E-H_P_20_2353__NODE_543_length_55561_cov_110.091342 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.1999 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139674 SAMEA13537704 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738207. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537704 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 83.3698 MAG coverage software Reads (ERR7738207) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 428 Submitter Id Hadza_MoBio_hadza-E-H_N_22_2341__NODE_217_length_90301_cov_47.823373_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7931034482758621 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586211 sample name Hadza_MoBio_hadza-E-H_N_22_2341__NODE_217_length_90301_cov_47.823373_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.500 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139675 SAMEA13537705 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738207. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537705 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 222.477 MAG coverage software Reads (ERR7738207) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 248 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_MoBio_hadza-E-H_N_22_2341__NODE_67_length_156420_cov_129.018024_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; HMM-based (lower-bound) completeness score 71.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586211 sample name Hadza_MoBio_hadza-E-H_N_22_2341__NODE_67_length_156420_cov_129.018024_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139676 SAMEA13537706 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738207. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537706 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 398.304 MAG coverage software Reads (ERR7738207) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_N_22_2341__NODE_1218_length_34575_cov_222.052931 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586211 sample name Hadza_MoBio_hadza-E-H_N_22_2341__NODE_1218_length_34575_cov_222.052931 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME079077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000434935 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.2011 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139677 SAMEA13537707 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738207. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537707 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 20.3827 MAG coverage software Reads (ERR7738207) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 158 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_N_22_2341__NODE_1827_length_25117_cov_12.071086 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586211 sample name Hadza_MoBio_hadza-E-H_N_22_2341__NODE_1827_length_25117_cov_12.071086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139678 SAMEA13537708 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738207. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537708 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 12.8869 MAG coverage software Reads (ERR7738207) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 173 Submitter Id Hadza_MoBio_hadza-E-H_N_22_2341__NODE_329_length_74051_cov_7.546530 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6851851851851852 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586211 sample name Hadza_MoBio_hadza-E-H_N_22_2341__NODE_329_length_74051_cov_7.546530 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000247 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter;s__Intestinibacter bartlettii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.561 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139679 SAMEA13537709 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738207. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537709 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 16.9103 MAG coverage software Reads (ERR7738207) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559675) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_MoBio_hadza-E-H_N_22_2341__NODE_899_length_42016_cov_9.737333 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586211 sample name Hadza_MoBio_hadza-E-H_N_22_2341__NODE_899_length_42016_cov_9.737333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738207_virus.899 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139680 SAMEA13537710 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738208. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537710 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 15.4815 MAG coverage software Reads (ERR7738208) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561203) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-A-D_D_12_1619__NODE_1523_length_31651_cov_9.379299_1 Viral contig found in MAG ERR7738208_bin.198 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585868 sample name Hadza_MoBio_hadza-A-D_D_12_1619__NODE_1523_length_31651_cov_9.379299_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.1495 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139681 SAMEA13537711 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738208. BACPHLIP temperate score 0.1474118942731278 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537711 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 28.5793 MAG coverage software Reads (ERR7738208) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561203) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 237 Submitter Id Hadza_MoBio_hadza-A-D_D_12_1619__NODE_64_length_157246_cov_18.312835_1 Viral contig found in MAG ERR7738208_bin.212 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9803921568627452 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585868 sample name Hadza_MoBio_hadza-A-D_D_12_1619__NODE_64_length_157246_cov_18.312835_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME212098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738208_provirus.64 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139682 SAMEA13537712 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738208. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537712 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 10.789 MAG coverage software Reads (ERR7738208) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561203) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_D_12_1619__NODE_1446_length_32709_cov_6.418209 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585868 sample name Hadza_MoBio_hadza-A-D_D_12_1619__NODE_1446_length_32709_cov_6.418209 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.3424238 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139683 SAMEA13537713 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738208. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537713 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 31.9602 MAG coverage software Reads (ERR7738208) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561203) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 104 Number of CRISPR spacer hits supporting host taxonomy 110 Submitter Id Hadza_MoBio_hadza-A-D_D_12_1619__NODE_1778_length_28463_cov_19.316670 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585868 sample name Hadza_MoBio_hadza-A-D_D_12_1619__NODE_1778_length_28463_cov_19.316670 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.1890 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139684 SAMEA13537714 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738208. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537714 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 18.7008 MAG coverage software Reads (ERR7738208) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561203) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 299 Submitter Id Hadza_MoBio_hadza-A-D_D_12_1619__NODE_415_length_68588_cov_11.172556 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585868 sample name Hadza_MoBio_hadza-A-D_D_12_1619__NODE_415_length_68588_cov_11.172556 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_virus.237 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139685 SAMEA13537715 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738208. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537715 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 47.627 MAG coverage software Reads (ERR7738208) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561203) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 182 Submitter Id Hadza_MoBio_hadza-A-D_D_12_1619__NODE_932_length_41986_cov_28.238087 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585868 sample name Hadza_MoBio_hadza-A-D_D_12_1619__NODE_932_length_41986_cov_28.238087 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746721_virus.430 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139686 SAMEA13537716 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae provirus assembled from ERR7738209. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537716 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 9.12072 MAG coverage software Reads (ERR7738209) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560053) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-E-H_B_2_2152__NODE_1377_length_47774_cov_5.300501_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586138 sample name Hadza_MoBio_hadza-E-H_B_2_2152__NODE_1377_length_47774_cov_5.300501_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_virus.602 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11139687 SAMEA13537717 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738209. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537717 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 62.7712 MAG coverage software Reads (ERR7738209) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560053) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 217 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_B_2_2152__NODE_623_length_86156_cov_37.223492_1 Viral contig found in MAG ERR7738209_bin.5 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586138 sample name Hadza_MoBio_hadza-E-H_B_2_2152__NODE_623_length_86156_cov_37.223492_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_provirus.996 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139688 SAMEA13537718 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738209. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537718 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 124.318 MAG coverage software Reads (ERR7738209) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560053) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_B_2_2152__NODE_1223_length_53119_cov_70.731477 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; HMM-based (lower-bound) completeness score 63.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6041666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586138 sample name Hadza_MoBio_hadza-E-H_B_2_2152__NODE_1223_length_53119_cov_70.731477 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738209_virus.1223 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139689 SAMEA13537719 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738209. BACPHLIP temperate score 0.45 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537719 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 54.9438 MAG coverage software Reads (ERR7738209) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560053) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 582 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_B_2_2152__NODE_2084_length_32066_cov_38.951390 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586138 sample name Hadza_MoBio_hadza-E-H_B_2_2152__NODE_2084_length_32066_cov_38.951390 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738209_virus.2084 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139690 SAMEA13537720 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738209. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537720 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 138.883 MAG coverage software Reads (ERR7738209) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560053) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_B_2_2152__NODE_3545_length_18254_cov_79.818837 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; HMM-based (lower-bound) completeness score 62.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586138 sample name Hadza_MoBio_hadza-E-H_B_2_2152__NODE_3545_length_18254_cov_79.818837 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_virus.2030 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139691 SAMEA13537721 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738209. BACPHLIP temperate score 0.525 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537721 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 47.0548 MAG coverage software Reads (ERR7738209) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560053) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 188 Number of CRISPR spacer hits supporting host taxonomy 109 Submitter Id Hadza_MoBio_hadza-E-H_B_2_2152__NODE_751_length_76468_cov_27.710084 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8648648648648649 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586138 sample name Hadza_MoBio_hadza-E-H_B_2_2152__NODE_751_length_76468_cov_27.710084 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737972_virus.307 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139692 SAMEA13537722 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738210. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537722 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 62.4093 MAG coverage software Reads (ERR7738210) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560447) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 199 Number of CRISPR spacer hits supporting host taxonomy 136 Submitter Id Hadza_MoBio_hadza-E-H_E_12_1851__NODE_283_length_73848_cov_38.565900_1 Viral contig found in MAG ERR7738210_bin.105 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586036 sample name Hadza_MoBio_hadza-E-H_E_12_1851__NODE_283_length_73848_cov_38.565900_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139693 SAMEA13537723 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738210. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537723 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 57.6376 MAG coverage software Reads (ERR7738210) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560447) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_E_12_1851__NODE_87_length_122087_cov_35.740775_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5588235294117647 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586036 sample name Hadza_MoBio_hadza-E-H_E_12_1851__NODE_87_length_122087_cov_35.740775_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745675_virus.89 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139694 SAMEA13537724 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738210. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537724 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 11.6652 MAG coverage software Reads (ERR7738210) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560447) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 54 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-E-H_E_12_1851__NODE_1426_length_25639_cov_7.132853 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586036 sample name Hadza_MoBio_hadza-E-H_E_12_1851__NODE_1426_length_25639_cov_7.132853 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738210_virus.1426 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139695 SAMEA13537725 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738210. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537725 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 25.8559 MAG coverage software Reads (ERR7738210) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560447) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_E_12_1851__NODE_514_length_52443_cov_15.930298 Viral contig found in MAG ERR7738210_bin.79 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.56 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586036 sample name Hadza_MoBio_hadza-E-H_E_12_1851__NODE_514_length_52443_cov_15.930298 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_virus.780 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139696 SAMEA13537726 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738211. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537726 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 40.8304 MAG coverage software Reads (ERR7738211) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_G_21_2445__NODE_1254_length_29216_cov_23.738769_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586239 sample name Hadza_MoBio_hadza-I-L_G_21_2445__NODE_1254_length_29216_cov_23.738769_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.1468 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139697 SAMEA13537727 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738211. BACPHLIP temperate score 0.2060434728913873 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537727 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 308.889 MAG coverage software Reads (ERR7738211) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 190 Submitter Id Hadza_MoBio_hadza-I-L_G_21_2445__NODE_75_length_124500_cov_263.356526_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586239 sample name Hadza_MoBio_hadza-I-L_G_21_2445__NODE_75_length_124500_cov_263.356526_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.2104 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139698 SAMEA13537728 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738211. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537728 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 17.2868 MAG coverage software Reads (ERR7738211) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-I-L_G_21_2445__NODE_25_length_189795_cov_9.923286 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586239 sample name Hadza_MoBio_hadza-I-L_G_21_2445__NODE_25_length_189795_cov_9.923286 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.115 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139699 SAMEA13537729 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738211. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537729 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 15.9739 MAG coverage software Reads (ERR7738211) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 337 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-I-L_G_21_2445__NODE_644_length_47045_cov_9.104305 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586239 sample name Hadza_MoBio_hadza-I-L_G_21_2445__NODE_644_length_47045_cov_9.104305 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139700 SAMEA13537730 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738212. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537730 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 57.501 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_10_length_367401_cov_33.805834_1 Viral contig found in MAG ERR7738212_bin.202 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_10_length_367401_cov_33.805834_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270963 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;s__Lachnospira sp900545725 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746012_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139701 SAMEA13537731 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738212. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537731 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 72.8989 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 267 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_233_length_102099_cov_82.089785_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5862068965517241 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_233_length_102099_cov_82.089785_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139702 SAMEA13537732 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738212. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537732 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 12.9033 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 62 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_649_length_61041_cov_7.466603_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 42.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_649_length_61041_cov_7.466603_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.267 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139703 SAMEA13537733 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738212. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537733 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 18.156 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 82 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_1221_length_41156_cov_10.597775 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8484848484848485 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_1221_length_41156_cov_10.597775 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_virus.1221 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139704 SAMEA13537734 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738212. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537734 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 15.8476 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_1630_length_33415_cov_9.282710 Viral contig found in MAG ERR7738212_bin.201 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_1630_length_33415_cov_9.282710 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738233_virus.443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139705 SAMEA13537735 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738212. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537735 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 7.60892 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_2086_length_27968_cov_4.036284 Viral contig found in MAG ERR7738212_bin.145 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_2086_length_27968_cov_4.036284 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME254156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-582;s__CAG-582 sp000435515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_virus.2086 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139706 SAMEA13537736 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738212. BACPHLIP temperate score 0.25495594713656383 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537736 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 9.33836 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_239_length_101285_cov_5.336436 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_239_length_101285_cov_5.336436 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124703 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738531_virus.150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139707 SAMEA13537737 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738212. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537737 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 37.1092 MAG coverage software Reads (ERR7738212) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559763) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_P_10_2358__NODE_663_length_60238_cov_21.196622 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9428571428571428 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_MoBio_hadza-I-L_P_10_2358__NODE_663_length_60238_cov_21.196622 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738148_bin.16 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp900544615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.1752 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139708 SAMEA13537738 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738213. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537738 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 11.2392 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 60 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1202_length_45576_cov_6.658806_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.45 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1202_length_45576_cov_6.658806_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745397_provirus.167 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139709 SAMEA13537739 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738213. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537739 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 74.7189 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_278_length_107566_cov_45.070603_1 Viral contig found in MAG ERR7738213_bin.135 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_278_length_107566_cov_45.070603_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0296258 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139710 SAMEA13537740 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738213. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537740 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 17.2904 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_71_length_213615_cov_9.913383_1 Viral contig found in MAG ERR7738213_bin.174 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_71_length_213615_cov_9.913383_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139711 SAMEA13537741 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738213. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537741 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 8.46637 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1113_length_48041_cov_4.807043 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1113_length_48041_cov_4.807043 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139712 SAMEA13537742 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738213. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537742 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 15.7437 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 73 Number of CRISPR spacer hits supporting host taxonomy 287 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1393_length_41489_cov_9.026007 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1393_length_41489_cov_9.026007 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139713 SAMEA13537743 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738213. BACPHLIP temperate score 0.575 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537743 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 12.6241 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1729_length_35331_cov_7.300051 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_1729_length_35331_cov_7.300051 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME222400 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1227;s__UBA1227 sp900545655 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738213_virus.1729 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139714 SAMEA13537744 2133760 Siphoviridae environmental samples This sample represents an uncultured Phietavirus virus assembled from ERR7738213. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537744 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 13.0437 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_2248_length_28739_cov_7.637290 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7407407407407407 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_2248_length_28739_cov_7.637290 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738213_virus.2248 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Azeredovirinae; Phietavirus virus enrichment approach none ERS11139715 SAMEA13537745 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738213. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537745 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 9.67049 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 275 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_3363_length_20301_cov_5.631972 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_3363_length_20301_cov_5.631972 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.865 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139716 SAMEA13537746 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738213. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537746 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 59.2167 MAG coverage software Reads (ERR7738213) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561379) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 153 Submitter Id Hadza_MoBio_hadza-A-D_P_13_1506__NODE_982_length_51996_cov_35.131994 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585762 sample name Hadza_MoBio_hadza-A-D_P_13_1506__NODE_982_length_51996_cov_35.131994 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.1048 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139717 SAMEA13537747 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738214. BACPHLIP temperate score 0.08468667725817124 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537747 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 32.6087 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_596_length_49475_cov_19.843313_1 Viral contig found in MAG ERR7738214_bin.85 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_596_length_49475_cov_19.843313_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.627 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139718 SAMEA13537748 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738214. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537748 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 96.1432 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_1157_length_31088_cov_61.196962 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_1157_length_31088_cov_61.196962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME099131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000435075 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.2151 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139719 SAMEA13537749 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738214. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537749 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 2830.94 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_157_length_106893_cov_1698.004419 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.954954954954955 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_157_length_106893_cov_1698.004419 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_virus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11139720 SAMEA13537750 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738214. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537750 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 1658.63 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_216_length_91873_cov_1005.649375 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4888888888888889 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_216_length_91873_cov_1005.649375 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.216 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139721 SAMEA13537751 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738214. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537751 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 20.641 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_2606_length_17170_cov_12.708645 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; HMM-based (lower-bound) completeness score 57.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_2606_length_17170_cov_12.708645 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.2606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139722 SAMEA13537752 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738214. BACPHLIP temperate score 0.03986784140969163 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537752 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 10.2504 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_3431_length_13693_cov_6.115977 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_3431_length_13693_cov_6.115977 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.3431 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139723 SAMEA13537753 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738214. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537753 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 11.0656 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 94 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_477_length_57213_cov_6.673393 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_477_length_57213_cov_6.673393 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.477 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139724 SAMEA13537754 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738214. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537754 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 13.7652 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_653_length_47213_cov_8.213531 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_653_length_47213_cov_8.213531 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746741_bin.80 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;s__RUG572 sp900547945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.1666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139725 SAMEA13537755 2100421 uncultured Caudovirales phage This sample represents an uncultured unclassified Braunvirinae virus assembled from ERR7738214. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537755 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 19.977 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_730_length_43799_cov_12.139312 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6612903225806451 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_730_length_43799_cov_12.139312 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME108563 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789;s__UBA3789 sp900543055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.730 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Drexlerviridae; Braunvirinae; unclassified Braunvirinae virus enrichment approach none ERS11139726 SAMEA13537756 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738214. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537756 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 264.724 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 79 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_809_length_41186_cov_160.454426 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_809_length_41186_cov_160.454426 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.1502 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139727 SAMEA13537757 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738214. BACPHLIP temperate score 0.3799559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537757 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 10.9648 MAG coverage software Reads (ERR7738214) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560007) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 106 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_H_11_1999__NODE_929_length_36798_cov_6.739876 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586102 sample name Hadza_MoBio_hadza-E-H_H_11_1999__NODE_929_length_36798_cov_6.739876 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.1480 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139728 SAMEA13537758 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738215. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537758 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 22.4291 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_191_length_113756_cov_12.688227_1 Viral contig found in MAG ERR7738215_bin.122 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_191_length_113756_cov_12.688227_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738227_bin.197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp004557855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738215_provirus.191 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139729 SAMEA13537759 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738215. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537759 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 8.47383 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 145 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_653_length_58333_cov_4.670437_1 Viral contig found in MAG ERR7738215_bin.187 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_653_length_58333_cov_4.670437_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_provirus.4_2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139730 SAMEA13537760 336724 Myoviridae environmental samples This sample represents an uncultured Bdellovibrio phage phi1422 virus assembled from ERR7738215. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537760 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 66.9552 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_1150_length_40983_cov_36.766049 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_1150_length_40983_cov_36.766049 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.804 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Bdellovibrio phage phi1422 virus enrichment approach none ERS11139731 SAMEA13537761 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738215. BACPHLIP temperate score 0.7573237885462554 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537761 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 20.4647 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_1479_length_34997_cov_11.690092 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_1479_length_34997_cov_11.690092 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.1676 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139732 SAMEA13537762 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738215. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537762 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 14.27 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_2080_length_27438_cov_8.758598 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_2080_length_27438_cov_8.758598 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738215_virus.2080 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139733 SAMEA13537763 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738215. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537763 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 36.0491 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_2737_length_22454_cov_22.705054 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_2737_length_22454_cov_22.705054 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_provirus.2080 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139734 SAMEA13537764 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738215. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537764 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 8.17249 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_550_length_64358_cov_4.654361 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48148148148148145 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_550_length_64358_cov_4.654361 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738215_virus.550 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139735 SAMEA13537765 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738215. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537765 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 90.4241 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_697_length_56266_cov_50.974443 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_697_length_56266_cov_50.974443 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738215_virus.697 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139736 SAMEA13537766 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738215. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537766 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 18.0876 MAG coverage software Reads (ERR7738215) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561326) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_N_23_1309__NODE_924_length_47288_cov_10.214187 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585724 sample name Hadza_MoBio_hadza-I-L_N_23_1309__NODE_924_length_47288_cov_10.214187 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_provirus.148 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139737 SAMEA13537767 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738216. BACPHLIP temperate score 0.09849942002795124 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537767 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 14.6459 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_112_length_167225_cov_8.193828_1 Viral contig found in MAG ERR7738216_bin.96 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; HMM-based (lower-bound) completeness score 58.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_112_length_167225_cov_8.193828_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738216_bin.96 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1242;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738216_provirus.112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139738 SAMEA13537768 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738216. BACPHLIP temperate score 0.0322136563876652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537768 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 78.9345 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 84 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_268_length_121068_cov_49.286468_1 Viral contig found in MAG ERR7738216_bin.235 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_268_length_121068_cov_49.286468_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738216_provirus.268 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139739 SAMEA13537769 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738216. BACPHLIP temperate score 0.03986784140969163 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537769 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 42.3683 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_684_length_70316_cov_24.025627_1 Viral contig found in MAG ERR7738216_bin.242 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_684_length_70316_cov_24.025627_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME258969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__CAG-269 sp001916005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738216_provirus.684 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139740 SAMEA13537770 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738216. BACPHLIP temperate score 0.00505093710516759 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537770 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 101.543 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_1083_length_53347_cov_60.109499 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_1083_length_53347_cov_60.109499 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.981 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139741 SAMEA13537771 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738216. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537771 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 40.2982 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_169_length_146589_cov_23.530489 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 31 number of unique standard tRNAs extracted 19 percent of BLAST hits supporting viral taxonomy 0.6981132075471698 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_169_length_146589_cov_23.530489 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.887873 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139742 SAMEA13537772 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738216. BACPHLIP temperate score 0.3673458149779736 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537772 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 15.7134 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_2187_length_31039_cov_9.066178 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_2187_length_31039_cov_9.066178 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747426_bin.316 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D succinifaciens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.684 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139743 SAMEA13537773 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738216. BACPHLIP temperate score 0.06798872201629169 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537773 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 94.8811 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_4002_length_18414_cov_56.033484 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_4002_length_18414_cov_56.033484 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738216_virus.4002 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139744 SAMEA13537774 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738216. BACPHLIP temperate score 0.1424559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537774 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 37.055 MAG coverage software Reads (ERR7738216) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559673) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_N_16_2338__NODE_91_length_181664_cov_21.462566 Viral contig found in MAG ERR7738216_bin.225 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 13 number of unique standard tRNAs extracted 11 percent of BLAST hits supporting viral taxonomy 0.5681818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586208 sample name Hadza_MoBio_hadza-E-H_N_16_2338__NODE_91_length_181664_cov_21.462566 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738216_virus.91 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11139745 SAMEA13537775 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738217. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537775 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 17.2561 MAG coverage software Reads (ERR7738217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_H_A_11_2177__NODE_486_length_61862_cov_9.732055_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_H_A_11_2177__NODE_486_length_61862_cov_9.732055_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738217_provirus.486 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11139746 SAMEA13537776 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738217. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537776 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 14.6248 MAG coverage software Reads (ERR7738217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 127 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_H_A_11_2177__NODE_1158_length_35319_cov_8.200159 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_H_A_11_2177__NODE_1158_length_35319_cov_8.200159 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738217_virus.1158 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139747 SAMEA13537777 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738217. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537777 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 11.7209 MAG coverage software Reads (ERR7738217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 107 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_H_A_11_2177__NODE_1451_length_30061_cov_6.436233 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_H_A_11_2177__NODE_1451_length_30061_cov_6.436233 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_provirus.18 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139748 SAMEA13537778 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738217. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537778 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 12.8713 MAG coverage software Reads (ERR7738217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_H_A_11_2177__NODE_2552_length_19880_cov_7.096147 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_H_A_11_2177__NODE_2552_length_19880_cov_7.096147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025308 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.2492 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139749 SAMEA13537779 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738217. BACPHLIP temperate score 0.17129856875493005 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537779 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 9.15339 MAG coverage software Reads (ERR7738217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_H_A_11_2177__NODE_749_length_46614_cov_4.984700 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_H_A_11_2177__NODE_749_length_46614_cov_4.984700 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-884;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.777 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139750 SAMEA13537780 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738218. BACPHLIP temperate score 0.12085444902106184 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537780 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 21.4516 MAG coverage software Reads (ERR7738218) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561078) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_F_1_1575__NODE_151_length_98797_cov_10.954021_1 Viral contig found in MAG ERR7738218_bin.68 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585824 sample name Hadza_MoBio_hadza-A-D_F_1_1575__NODE_151_length_98797_cov_10.954021_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738595_bin.190 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_provirus.47 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139751 SAMEA13537781 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7738218. BACPHLIP temperate score 0.24245594713656385 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537781 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 13.1435 MAG coverage software Reads (ERR7738218) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561078) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_F_1_1575__NODE_93_length_123700_cov_7.363411_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9295774647887324 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585824 sample name Hadza_MoBio_hadza-A-D_F_1_1575__NODE_93_length_123700_cov_7.363411_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124703 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_provirus.93 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139752 SAMEA13537782 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738218. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537782 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 11.9022 MAG coverage software Reads (ERR7738218) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561078) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-A-D_F_1_1575__NODE_1283_length_28067_cov_6.239728 Viral contig found in MAG ERR7738218_bin.84 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585824 sample name Hadza_MoBio_hadza-A-D_F_1_1575__NODE_1283_length_28067_cov_6.239728 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_virus.1283 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139753 SAMEA13537783 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738218. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537783 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 11.8808 MAG coverage software Reads (ERR7738218) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561078) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_F_1_1575__NODE_2619_length_15756_cov_6.463715 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 85.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585824 sample name Hadza_MoBio_hadza-A-D_F_1_1575__NODE_2619_length_15756_cov_6.463715 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_virus.2619 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139754 SAMEA13537784 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738218. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537784 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 126.323 MAG coverage software Reads (ERR7738218) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561078) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Hadza_MoBio_hadza-A-D_F_1_1575__NODE_432_length_58693_cov_68.560035 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9583333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585824 sample name Hadza_MoBio_hadza-A-D_F_1_1575__NODE_432_length_58693_cov_68.560035 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11139755 SAMEA13537785 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738218. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537785 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 20.1053 MAG coverage software Reads (ERR7738218) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561078) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-A-D_F_1_1575__NODE_714_length_42926_cov_10.770310 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585824 sample name Hadza_MoBio_hadza-A-D_F_1_1575__NODE_714_length_42926_cov_10.770310 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_virus.714 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139756 SAMEA13537786 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738218. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537786 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 13.097 MAG coverage software Reads (ERR7738218) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561078) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-A-D_F_1_1575__NODE_935_length_35715_cov_6.984399 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585824 sample name Hadza_MoBio_hadza-A-D_F_1_1575__NODE_935_length_35715_cov_6.984399 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.2577 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139757 SAMEA13537787 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738219. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537787 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 46.1503 MAG coverage software Reads (ERR7738219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561625) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_D_14_1184__NODE_208_length_85237_cov_30.147839_1 Viral contig found in MAG ERR7738219_bin.99 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_MoBio_hadza-I-L_D_14_1184__NODE_208_length_85237_cov_30.147839_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738251_provirus.273 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139758 SAMEA13537788 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738219. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537788 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 67.2942 MAG coverage software Reads (ERR7738219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561625) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 79 Submitter Id Hadza_MoBio_hadza-I-L_D_14_1184__NODE_572_length_47091_cov_43.551304_1 Viral contig found in MAG ERR7738219_bin.71 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_MoBio_hadza-I-L_D_14_1184__NODE_572_length_47091_cov_43.551304_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738228_provirus.378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139759 SAMEA13537789 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738219. BACPHLIP temperate score 0.2693548984968848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537789 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 11.6848 MAG coverage software Reads (ERR7738219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561625) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_D_14_1184__NODE_1826_length_22838_cov_7.139976 Viral contig found in MAG ERR7738219_bin.22 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_MoBio_hadza-I-L_D_14_1184__NODE_1826_length_22838_cov_7.139976 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_virus.1846 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139760 SAMEA13537790 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738219. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537790 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 172.418 MAG coverage software Reads (ERR7738219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561625) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_D_14_1184__NODE_4087_length_13317_cov_104.536254 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_MoBio_hadza-I-L_D_14_1184__NODE_4087_length_13317_cov_104.536254 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.4087 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11139761 SAMEA13537791 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738219. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537791 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 19.9911 MAG coverage software Reads (ERR7738219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561625) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-I-L_D_14_1184__NODE_685_length_42779_cov_12.465365 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_MoBio_hadza-I-L_D_14_1184__NODE_685_length_42779_cov_12.465365 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0316936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139762 SAMEA13537792 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738219. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537792 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 28.5986 MAG coverage software Reads (ERR7738219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561625) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_D_14_1184__NODE_886_length_36733_cov_17.011703 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_MoBio_hadza-I-L_D_14_1184__NODE_886_length_36733_cov_17.011703 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.1558 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139763 SAMEA13537793 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738221. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537793 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 65.2642 MAG coverage software Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 171 Number of CRISPR spacer hits supporting host taxonomy 166 Submitter Id Hadza_MoBio_hadza-I-L_N_19_1307__NODE_318_length_67879_cov_38.061606_1 Viral contig found in MAG ERR7738221_bin.119 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_MoBio_hadza-I-L_N_19_1307__NODE_318_length_67879_cov_38.061606_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_provirus.106 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139764 SAMEA13537794 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage provirus assembled from ERR7738221. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537794 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 14.5572 MAG coverage software Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-I-L_N_19_1307__NODE_65_length_136577_cov_8.420374_1 Viral contig found in MAG ERR7738221_bin.126 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_MoBio_hadza-I-L_N_19_1307__NODE_65_length_136577_cov_8.420374_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270564 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738141_virus.327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11139765 SAMEA13537795 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738221. BACPHLIP temperate score 0.0680097705694487 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537795 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 55.5287 MAG coverage software Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_N_19_1307__NODE_133_length_100444_cov_30.890382 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 12 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_MoBio_hadza-I-L_N_19_1307__NODE_133_length_100444_cov_30.890382 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.320 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139766 SAMEA13537796 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738221. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537796 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 7.22957 MAG coverage software Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_N_19_1307__NODE_2231_length_18027_cov_3.850919 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_MoBio_hadza-I-L_N_19_1307__NODE_2231_length_18027_cov_3.850919 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738221_virus.2231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139767 SAMEA13537797 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738221. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537797 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 34.2385 MAG coverage software Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-I-L_N_19_1307__NODE_528_length_51747_cov_19.049758 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_MoBio_hadza-I-L_N_19_1307__NODE_528_length_51747_cov_19.049758 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_provirus.890 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139768 SAMEA13537798 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738221. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537798 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 13.492 MAG coverage software Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_N_19_1307__NODE_753_length_41629_cov_7.733707 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42105263157894735 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_MoBio_hadza-I-L_N_19_1307__NODE_753_length_41629_cov_7.733707 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_virus.1341 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139769 SAMEA13537799 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738221. BACPHLIP temperate score 0.1074339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537799 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 34.992 MAG coverage software Reads (ERR7738221) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_N_19_1307__NODE_914_length_36773_cov_20.821479 Viral contig found in MAG ERR7738221_bin.98 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_MoBio_hadza-I-L_N_19_1307__NODE_914_length_36773_cov_20.821479 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738221_virus.914 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139770 SAMEA13537800 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738222. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537800 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 32.5975 MAG coverage software Reads (ERR7738222) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561039) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 159 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_F_2_1565__NODE_456_length_67045_cov_18.966596_1 Viral contig found in MAG ERR7738222_bin.102 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585819 sample name Hadza_MoBio_C-REDO_F_2_1565__NODE_456_length_67045_cov_18.966596_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_provirus.617 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139771 SAMEA13537801 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738222. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537801 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 13.1696 MAG coverage software Reads (ERR7738222) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561039) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 424 Submitter Id Hadza_MoBio_C-REDO_F_2_1565__NODE_1175_length_35270_cov_7.492626 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585819 sample name Hadza_MoBio_C-REDO_F_2_1565__NODE_1175_length_35270_cov_7.492626 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.865 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139772 SAMEA13537802 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738222. BACPHLIP temperate score 0.25781851150140056 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537802 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 10.037 MAG coverage software Reads (ERR7738222) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561039) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 237 Submitter Id Hadza_MoBio_C-REDO_F_2_1565__NODE_1862_length_25926_cov_5.688731 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585819 sample name Hadza_MoBio_C-REDO_F_2_1565__NODE_1862_length_25926_cov_5.688731 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746344_virus.405 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11139773 SAMEA13537803 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738222. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537803 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 7.88742 MAG coverage software Reads (ERR7738222) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561039) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_C-REDO_F_2_1565__NODE_2550_length_21104_cov_4.391972 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585819 sample name Hadza_MoBio_C-REDO_F_2_1565__NODE_2550_length_21104_cov_4.391972 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_provirus.1362 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139774 SAMEA13537804 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7738222. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537804 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 10.4661 MAG coverage software Reads (ERR7738222) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561039) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 185 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_C-REDO_F_2_1565__NODE_571_length_58446_cov_5.953914 Viral contig found in MAG ERR7738222_bin.70 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8787878787878788 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585819 sample name Hadza_MoBio_C-REDO_F_2_1565__NODE_571_length_58446_cov_5.953914 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_C vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_provirus.687 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11139775 SAMEA13537805 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738222. BACPHLIP temperate score 0.03997797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537805 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 7.6939 MAG coverage software Reads (ERR7738222) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561039) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_F_2_1565__NODE_8021_length_9062_cov_4.145019 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585819 sample name Hadza_MoBio_C-REDO_F_2_1565__NODE_8021_length_9062_cov_4.145019 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_virus.6778 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139776 SAMEA13537806 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738223. BACPHLIP temperate score 0.13558963045632055 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537806 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 9.76893 MAG coverage software Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_A_8_1817__NODE_14466_length_6503_cov_9.445534_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-27 completeness approach CheckV; HMM-based (lower-bound) completeness score 77.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586017 sample name Hadza_MoBio_hadza-E-H_A_8_1817__NODE_14466_length_6503_cov_9.445534_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME276106 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900548615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738223_provirus.14466 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139777 SAMEA13537807 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738223. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537807 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 13.3078 MAG coverage software Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 65 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_A_8_1817__NODE_535_length_66803_cov_7.716048_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586017 sample name Hadza_MoBio_hadza-E-H_A_8_1817__NODE_535_length_66803_cov_7.716048_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253209 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-605;s__CAG-605 sp000433475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738223_provirus.535 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139778 SAMEA13537808 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738223. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537808 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 9.5145 MAG coverage software Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_A_8_1817__NODE_1051_length_45417_cov_5.455712 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586017 sample name Hadza_MoBio_hadza-E-H_A_8_1817__NODE_1051_length_45417_cov_5.455712 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738223_virus.1051 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139779 SAMEA13537809 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738223. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537809 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 8.9266 MAG coverage software Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-E-H_A_8_1817__NODE_1583_length_35123_cov_5.025253 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586017 sample name Hadza_MoBio_hadza-E-H_A_8_1817__NODE_1583_length_35123_cov_5.025253 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.2319 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139780 SAMEA13537810 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738223. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537810 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 105.243 MAG coverage software Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-E-H_A_8_1817__NODE_234_length_98991_cov_63.832339 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6170212765957447 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586017 sample name Hadza_MoBio_hadza-E-H_A_8_1817__NODE_234_length_98991_cov_63.832339 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738223_virus.234 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11139781 SAMEA13537811 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738223. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537811 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 12.9231 MAG coverage software Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 434 Number of CRISPR spacer hits supporting host taxonomy 494 Submitter Id Hadza_MoBio_hadza-E-H_A_8_1817__NODE_3085_length_21969_cov_7.598438 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586017 sample name Hadza_MoBio_hadza-E-H_A_8_1817__NODE_3085_length_21969_cov_7.598438 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.4695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139782 SAMEA13537812 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738223. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537812 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 41.4128 MAG coverage software Reads (ERR7738223) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560427) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_A_8_1817__NODE_720_length_56917_cov_25.295461 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586017 sample name Hadza_MoBio_hadza-E-H_A_8_1817__NODE_720_length_56917_cov_25.295461 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.821 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139783 SAMEA13537813 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738224. BACPHLIP temperate score 0.01734581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537813 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:21Z INSDC last update 2022-12-27T19:09:21Z INSDC status public MAG coverage depth 200.345 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3427 Number of CRISPR spacer hits supporting host taxonomy 374 Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_2_length_823501_cov_114.465922_1 Viral contig found in MAG ERR7738224_bin.13 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_2_length_823501_cov_114.465922_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_provirus.2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139784 SAMEA13537814 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis provirus assembled from ERR7738224. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537814 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 12.8917 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_692_length_58602_cov_7.484699_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.532258064516129 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_692_length_58602_cov_7.484699_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_provirus.692 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11139785 SAMEA13537815 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738224. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537815 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 15.1851 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 87 Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_1092_length_43188_cov_9.633133 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.696969696969697 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_1092_length_43188_cov_9.633133 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_virus.1092 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139786 SAMEA13537816 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738224. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537816 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 27.3226 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_1415_length_35280_cov_15.791836 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 54.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_1415_length_35280_cov_15.791836 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.1498 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139787 SAMEA13537817 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738224. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537817 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 8.36641 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_1980_length_27447_cov_4.532737 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_1980_length_27447_cov_4.532737 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1814 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139788 SAMEA13537818 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738224. BACPHLIP temperate score 0.17129856875493005 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537818 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 8.19774 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_2593_length_21779_cov_4.498341 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_2593_length_21779_cov_4.498341 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.2249 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139789 SAMEA13537819 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738224. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537819 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 18.4742 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 100 Number of CRISPR spacer hits supporting host taxonomy 188 Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_511_length_72925_cov_20.684315 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.8372093023255814 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_511_length_72925_cov_20.684315 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253237 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465;s__CAG-465 sp000433755 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_virus.511 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139790 SAMEA13537820 340016 uncultured virus This sample represents an uncultured Klebsiella phage P-K7R virus assembled from ERR7738224. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537820 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 34.0878 MAG coverage software Reads (ERR7738224) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560526) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_M_20_1921__NODE_812_length_52543_cov_19.677944 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7804878048780488 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586064 sample name Hadza_MoBio_hadza-E-H_M_20_1921__NODE_812_length_52543_cov_19.677944 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_virus.812 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Klebsiella phage P-K7R virus enrichment approach none ERS11139791 SAMEA13537821 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738225. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537821 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 100.103 MAG coverage software Reads (ERR7738225) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559286) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_hadza-I-L_C_20_2577__NODE_321_length_65221_cov_61.655425_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586301 sample name Hadza_MoBio_hadza-I-L_C_20_2577__NODE_321_length_65221_cov_61.655425_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738225_provirus.321 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139792 SAMEA13537822 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738225. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537822 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 24.3035 MAG coverage software Reads (ERR7738225) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559286) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 156 Submitter Id Hadza_MoBio_hadza-I-L_C_20_2577__NODE_120_length_104417_cov_13.885327 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.2857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586301 sample name Hadza_MoBio_hadza-I-L_C_20_2577__NODE_120_length_104417_cov_13.885327 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738225_virus.120 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139793 SAMEA13537823 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738225. BACPHLIP temperate score 0.04793421803331155 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537823 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 358.923 MAG coverage software Reads (ERR7738225) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559286) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_C_20_2577__NODE_22_length_181530_cov_202.432195 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.5192307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586301 sample name Hadza_MoBio_hadza-I-L_C_20_2577__NODE_22_length_181530_cov_202.432195 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.144 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139794 SAMEA13537824 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738225. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537824 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 30.4041 MAG coverage software Reads (ERR7738225) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559286) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 276 Submitter Id Hadza_MoBio_hadza-I-L_C_20_2577__NODE_637_length_44760_cov_18.146051 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.3636363636363637 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586301 sample name Hadza_MoBio_hadza-I-L_C_20_2577__NODE_637_length_44760_cov_18.146051 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738225_virus.637 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139795 SAMEA13537825 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738225. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537825 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 29.7493 MAG coverage software Reads (ERR7738225) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559286) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_C_20_2577__NODE_919_length_35410_cov_17.233917 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586301 sample name Hadza_MoBio_hadza-I-L_C_20_2577__NODE_919_length_35410_cov_17.233917 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME097668 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738225_virus.919 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139796 SAMEA13537826 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738226. BACPHLIP temperate score 0.777477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537826 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 22.6576 MAG coverage software Reads (ERR7738226) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561658) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 125 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-I-L_J_15_1254__NODE_77_length_138077_cov_12.614543_1 Viral contig found in MAG ERR7738226_bin.4 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585672 sample name Hadza_MoBio_hadza-I-L_J_15_1254__NODE_77_length_138077_cov_12.614543_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001120 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides thetaiotaomicron vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738175_provirus.46 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139797 SAMEA13537827 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738227. BACPHLIP temperate score 0.00743392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537827 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 17.1881 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 152 Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_292_length_76677_cov_9.602467_1 Viral contig found in MAG ERR7738227_bin.22 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_292_length_76677_cov_9.602467_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0319855 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139798 SAMEA13537828 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738227. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537828 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 263.733 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_67_length_161564_cov_161.874714_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_67_length_161564_cov_161.874714_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745625_provirus.431 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139799 SAMEA13537829 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7738227. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537829 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 8.69315 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 67 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_1325_length_30715_cov_4.979241 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_1325_length_30715_cov_4.979241 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME248826 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_D vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738534_provirus.448 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11139800 SAMEA13537830 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738227. BACPHLIP temperate score 0.00863157861825958 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537830 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 13.5812 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 250 Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_1823_length_24717_cov_8.113068 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_1823_length_24717_cov_8.113068 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.442 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139801 SAMEA13537831 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738227. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537831 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 37.503 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_2932_length_17383_cov_22.479140 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_2932_length_17383_cov_22.479140 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738534_virus.4069 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139802 SAMEA13537832 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738227. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537832 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 93.9281 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_501_length_57344_cov_56.630328 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_501_length_57344_cov_56.630328 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_virus.1262 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139803 SAMEA13537833 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738227. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537833 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 57.3845 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_709_length_46051_cov_34.659177 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_709_length_46051_cov_34.659177 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738167_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFHK01;s__SFHK01 sp004556395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745625_virus.630 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139804 SAMEA13537834 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738227. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537834 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 10.5297 MAG coverage software Reads (ERR7738227) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560982) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_H_3_1562__NODE_99_length_130676_cov_5.909563 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585816 sample name Hadza_MoBio_hadza-A-D_H_3_1562__NODE_99_length_130676_cov_5.909563 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME256853 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302;s__CAG-302 sp001916775 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_virus.36 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139805 SAMEA13537835 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738228. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537835 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 24.7128 MAG coverage software Reads (ERR7738228) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561052) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-A-D_F_23_1564__NODE_378_length_49176_cov_14.278336_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8709677419354839 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_MoBio_hadza-A-D_F_23_1564__NODE_378_length_49176_cov_14.278336_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738228_provirus.378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139806 SAMEA13537836 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738228. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537836 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 10.5133 MAG coverage software Reads (ERR7738228) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561052) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 319 Submitter Id Hadza_MoBio_hadza-A-D_F_23_1564__NODE_1433_length_23066_cov_6.366219 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_MoBio_hadza-A-D_F_23_1564__NODE_1433_length_23066_cov_6.366219 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.2064 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139807 SAMEA13537837 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738228. BACPHLIP temperate score 0.18564382477710456 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537837 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 12.4285 MAG coverage software Reads (ERR7738228) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561052) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_MoBio_hadza-A-D_F_23_1564__NODE_1865_length_19292_cov_7.516289 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_MoBio_hadza-A-D_F_23_1564__NODE_1865_length_19292_cov_7.516289 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737619_virus.813 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139808 SAMEA13537838 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738228. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537838 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 17.841 MAG coverage software Reads (ERR7738228) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561052) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_F_23_1564__NODE_343_length_51612_cov_10.759581 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5526315789473685 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_MoBio_hadza-A-D_F_23_1564__NODE_343_length_51612_cov_10.759581 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.170 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900768995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738228_virus.343 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139809 SAMEA13537839 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738228. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537839 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 37.4505 MAG coverage software Reads (ERR7738228) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561052) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 382 Number of CRISPR spacer hits supporting host taxonomy 129 Submitter Id Hadza_MoBio_hadza-A-D_F_23_1564__NODE_586_length_38862_cov_21.733222 Viral contig found in MAG ERR7738228_bin.92 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_MoBio_hadza-A-D_F_23_1564__NODE_586_length_38862_cov_21.733222 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738228_virus.586 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139810 SAMEA13537840 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738228. BACPHLIP temperate score 0.5875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537840 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 42.3045 MAG coverage software Reads (ERR7738228) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561052) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-A-D_F_23_1564__NODE_746_length_34276_cov_26.015264 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_MoBio_hadza-A-D_F_23_1564__NODE_746_length_34276_cov_26.015264 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.770 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139811 SAMEA13537841 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738229. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537841 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 24.9507 MAG coverage software Reads (ERR7738229) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567094) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 139 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_17_length_218050_cov_14.654544_1 Viral contig found in MAG ERR7738229_bin.5 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6904761904761905 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787339 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_17_length_218050_cov_14.654544_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738229_provirus.17 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139812 SAMEA13537842 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738229. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537842 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 73.9729 MAG coverage software Reads (ERR7738229) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567094) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_1182_length_28264_cov_43.322950 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787339 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_1182_length_28264_cov_43.322950 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139813 SAMEA13537843 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738229. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537843 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 147.192 MAG coverage software Reads (ERR7738229) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567094) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 408 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_253_length_76201_cov_85.863210 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.26666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787339 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_253_length_76201_cov_85.863210 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738229_virus.253 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139814 SAMEA13537844 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7738229. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537844 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 15.3023 MAG coverage software Reads (ERR7738229) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567094) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_6304_length_6393_cov_8.823939 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787339 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_6304_length_6393_cov_8.823939 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738229_virus.6304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11139815 SAMEA13537845 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738229. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537845 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 103.342 MAG coverage software Reads (ERR7738229) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567094) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 216 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_978_length_32862_cov_62.836328 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787339 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_11_CHE0009BZ__NODE_978_length_32862_cov_62.836328 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_provirus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139816 SAMEA13537846 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738230. BACPHLIP temperate score 0.14697136563876662 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537846 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 46.6614 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_351_length_91022_cov_33.720084_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_351_length_91022_cov_33.720084_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_provirus.872 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139817 SAMEA13537847 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738230. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537847 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 30.3616 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_96_length_173901_cov_27.375282_1 Viral contig found in MAG ERR7738230_bin.158 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_96_length_173901_cov_27.375282_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738230_bin.158 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_provirus.96 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139818 SAMEA13537848 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738230. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537848 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 66.7333 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_1190_length_40122_cov_38.121463 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_1190_length_40122_cov_38.121463 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.1823 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139819 SAMEA13537849 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738230. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537849 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 17.8234 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_1393_length_35871_cov_13.541404 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_1393_length_35871_cov_13.541404 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738274_bin.168 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__UBA1724;s__UBA1724 sp900548225 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_virus.1393 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139820 SAMEA13537850 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738230. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537850 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 29.201 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_172_length_133202_cov_16.675854 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_172_length_133202_cov_16.675854 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738580_bin.236 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668;s__UMGS1668 sp900553955 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.125 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139821 SAMEA13537851 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738230. BACPHLIP temperate score 0.1424559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537851 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 17.9763 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_2168_length_25682_cov_10.730795 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_2168_length_25682_cov_10.730795 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.2254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139822 SAMEA13537852 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738230. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537852 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 49.1908 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_27_length_276188_cov_28.168860 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.746268656716418 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_27_length_276188_cov_28.168860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745397_virus.34 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139824 SAMEA13537854 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738230. BACPHLIP temperate score 0.4875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537854 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 53.8318 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_692_length_58489_cov_30.540300 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4583333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_692_length_58489_cov_30.540300 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_virus.692 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139825 SAMEA13537855 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738230. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537855 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 8.32204 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_858_length_50607_cov_4.551079 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.34615384615384615 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_858_length_50607_cov_4.551079 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.1351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139826 SAMEA13537856 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738231. BACPHLIP temperate score 0.18997797356828192 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537856 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 832.154 MAG coverage software Reads (ERR7738231) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559570) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 160 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_B_23_2677__NODE_119_length_154447_cov_490.801173_1 Viral contig found in MAG ERR7738231_bin.10 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586375 sample name Hadza_MoBio_hadza-I-L_B_23_2677__NODE_119_length_154447_cov_490.801173_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139827 SAMEA13537857 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738231. BACPHLIP temperate score 0.1248898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537857 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 54.4798 MAG coverage software Reads (ERR7738231) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559570) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_B_23_2677__NODE_685_length_64838_cov_33.104337_1 Viral contig found in MAG ERR7738231_bin.148 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586375 sample name Hadza_MoBio_hadza-I-L_B_23_2677__NODE_685_length_64838_cov_33.104337_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_provirus.685 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11139828 SAMEA13537858 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738231. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537858 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 19.1721 MAG coverage software Reads (ERR7738231) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559570) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_B_23_2677__NODE_1219_length_45258_cov_11.574866 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586375 sample name Hadza_MoBio_hadza-I-L_B_23_2677__NODE_1219_length_45258_cov_11.574866 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.1948 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139829 SAMEA13537859 1478972 Gokushovirinae environmental samples This sample represents an uncultured Chlamydiamicrovirus virus assembled from ERR7738231. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537859 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 13.0171 MAG coverage software Reads (ERR7738231) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559570) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-I-L_B_23_2677__NODE_17462_length_5052_cov_8.104322 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586375 sample name Hadza_MoBio_hadza-I-L_B_23_2677__NODE_17462_length_5052_cov_8.104322 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738231_virus.17462 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; Chlamydiamicrovirus virus enrichment approach none ERS11139830 SAMEA13537860 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738231. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537860 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 107.56 MAG coverage software Reads (ERR7738231) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559570) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 266 Submitter Id Hadza_MoBio_hadza-I-L_B_23_2677__NODE_316_length_96312_cov_63.198098 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9583333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586375 sample name Hadza_MoBio_hadza-I-L_B_23_2677__NODE_316_length_96312_cov_63.198098 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139831 SAMEA13537861 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738231. BACPHLIP temperate score 0.06078698503890495 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537861 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 49.1405 MAG coverage software Reads (ERR7738231) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559570) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-I-L_B_23_2677__NODE_7124_length_11217_cov_29.490215 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586375 sample name Hadza_MoBio_hadza-I-L_B_23_2677__NODE_7124_length_11217_cov_29.490215 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME181333 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900540885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738231_virus.7124 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11139832 SAMEA13537862 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae provirus assembled from ERR7738232. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537862 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 30.6259 MAG coverage software Reads (ERR7738232) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560045) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_23_2151__NODE_124_length_152824_cov_18.796605_1 Viral contig found in MAG ERR7738232_bin.151 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586137 sample name Hadza_MoBio_hadza-E-H_P_23_2151__NODE_124_length_152824_cov_18.796605_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_provirus.435 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11139833 SAMEA13537863 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738232. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537863 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 34.1377 MAG coverage software Reads (ERR7738232) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560045) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 299 Submitter Id Hadza_MoBio_hadza-E-H_P_23_2151__NODE_246_length_109757_cov_21.597930_1 Viral contig found in MAG ERR7738232_bin.65 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586137 sample name Hadza_MoBio_hadza-E-H_P_23_2151__NODE_246_length_109757_cov_21.597930_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_provirus.246 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139834 SAMEA13537864 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738232. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537864 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 47.6397 MAG coverage software Reads (ERR7738232) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560045) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 659 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Hadza_MoBio_hadza-E-H_P_23_2151__NODE_474_length_76218_cov_34.741506_1 Viral contig found in MAG ERR7738232_bin.156 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 41.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586137 sample name Hadza_MoBio_hadza-E-H_P_23_2151__NODE_474_length_76218_cov_34.741506_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_provirus.131 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139835 SAMEA13537865 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738232. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537865 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 16.3489 MAG coverage software Reads (ERR7738232) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560045) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-E-H_P_23_2151__NODE_897_length_51050_cov_10.196280_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5675675675675675 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586137 sample name Hadza_MoBio_hadza-E-H_P_23_2151__NODE_897_length_51050_cov_10.196280_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_provirus.897 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139836 SAMEA13537866 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738232. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537866 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 20.6837 MAG coverage software Reads (ERR7738232) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560045) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_23_2151__NODE_1460_length_36358_cov_12.164494 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7317073170731707 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586137 sample name Hadza_MoBio_hadza-E-H_P_23_2151__NODE_1460_length_36358_cov_12.164494 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738260_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus;s__Lactiplantibacillus plantarum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_provirus.41 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139837 SAMEA13537867 2133760 Siphoviridae environmental samples This sample represents an uncultured Lactobacillus phage Sha1 virus assembled from ERR7738232. BACPHLIP temperate score 0.07489303048134302 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537867 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 34.8081 MAG coverage software Reads (ERR7738232) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560045) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_P_23_2151__NODE_2853_length_20537_cov_20.131623 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586137 sample name Hadza_MoBio_hadza-E-H_P_23_2151__NODE_2853_length_20537_cov_20.131623 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738260_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus;s__Lactiplantibacillus plantarum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_provirus.169 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lactobacillus phage Sha1 virus enrichment approach none ERS11139838 SAMEA13537868 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738232. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537868 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 59.77 MAG coverage software Reads (ERR7738232) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560045) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-E-H_P_23_2151__NODE_436_length_79977_cov_35.824856 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6585365853658537 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586137 sample name Hadza_MoBio_hadza-E-H_P_23_2151__NODE_436_length_79977_cov_35.824856 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_virus.436 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139839 SAMEA13537869 1701671 uncultured podovirus This sample represents an uncultured Roseobacter phage CRP-7 provirus assembled from ERR7738233. BACPHLIP temperate score 0.6873898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537869 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 95.0336 MAG coverage software Reads (ERR7738233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559747) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_P_8_2357__NODE_1037_length_41050_cov_54.623752_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586224 sample name Hadza_MoBio_hadza-I-L_P_8_2357__NODE_1037_length_41050_cov_54.623752_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.72 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Roseobacter phage CRP-7 virus enrichment approach none ERS11139840 SAMEA13537870 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738233. BACPHLIP temperate score 0.6125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537870 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 22.5358 MAG coverage software Reads (ERR7738233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559747) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-I-L_P_8_2357__NODE_34_length_242012_cov_13.079542_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586224 sample name Hadza_MoBio_hadza-I-L_P_8_2357__NODE_34_length_242012_cov_13.079542_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_provirus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139841 SAMEA13537871 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738233. BACPHLIP temperate score 0.22703565487607813 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537871 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 45.6796 MAG coverage software Reads (ERR7738233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559747) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_P_8_2357__NODE_731_length_51165_cov_27.420725_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586224 sample name Hadza_MoBio_hadza-I-L_P_8_2357__NODE_731_length_51165_cov_27.420725_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196;s__CAG-196 sp900553895 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.3054 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139842 SAMEA13537872 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738233. BACPHLIP temperate score 0.10914096916299568 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537872 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 17.3117 MAG coverage software Reads (ERR7738233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559747) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 73 Number of CRISPR spacer hits supporting host taxonomy 289 Submitter Id Hadza_MoBio_hadza-I-L_P_8_2357__NODE_1289_length_35470_cov_10.096658 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586224 sample name Hadza_MoBio_hadza-I-L_P_8_2357__NODE_1289_length_35470_cov_10.096658 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0331948 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139843 SAMEA13537873 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738233. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537873 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 31.4945 MAG coverage software Reads (ERR7738233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559747) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-I-L_P_8_2357__NODE_211_length_104148_cov_17.893630 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.9078947368421052 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586224 sample name Hadza_MoBio_hadza-I-L_P_8_2357__NODE_211_length_104148_cov_17.893630 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.368 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139845 SAMEA13537875 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7738233. BACPHLIP temperate score 0.18068787764054067 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537875 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 12.7271 MAG coverage software Reads (ERR7738233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559747) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_P_8_2357__NODE_734_length_51040_cov_7.219316 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.98 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586224 sample name Hadza_MoBio_hadza-I-L_P_8_2357__NODE_734_length_51040_cov_7.219316 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.389 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11139846 SAMEA13537876 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738234. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537876 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 24.649 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 447 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_177_length_131653_cov_14.515649_1 Viral contig found in MAG ERR7738234_bin.104 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9772727272727272 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_177_length_131653_cov_14.515649_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_provirus.177 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139847 SAMEA13537877 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738234. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537877 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 100.733 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_719_length_56732_cov_58.543712_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 85.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_719_length_56732_cov_58.543712_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_virus.1930 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139848 SAMEA13537878 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738234. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537878 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 7.9687 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_1193_length_40024_cov_4.431747 Viral contig found in MAG ERR7738234_bin.186 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_1193_length_40024_cov_4.431747 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139849 SAMEA13537879 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738234. BACPHLIP temperate score 0.07692912905635668 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537879 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 39.5383 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_1659_length_32015_cov_23.217014 Viral contig found in MAG ERR7738234_bin.69 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_1659_length_32015_cov_23.217014 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.2107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139850 SAMEA13537880 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738234. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537880 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 13.8778 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_2306_length_24642_cov_8.181111 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_2306_length_24642_cov_8.181111 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745434_virus.863 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139851 SAMEA13537881 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738234. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537881 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 10.6941 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_3399_length_17848_cov_6.129762 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_3399_length_17848_cov_6.129762 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.6060 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139853 SAMEA13537883 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738234. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537883 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 16.2481 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 188 Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_849_length_50300_cov_11.893993 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_849_length_50300_cov_11.893993 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_virus.849 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139854 SAMEA13537884 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738235. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537884 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 10.8418 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 241 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_1287_length_39994_cov_6.115916_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_1287_length_39994_cov_6.115916_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.2451 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139855 SAMEA13537885 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738235. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537885 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 17.5558 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_322_length_90806_cov_10.591531_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.575 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_322_length_90806_cov_10.591531_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_provirus.322 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139856 SAMEA13537886 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738235. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537886 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 11.0711 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_81_length_165907_cov_6.524706_1 Viral contig found in MAG ERR7738235_bin.97 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.6984126984126984 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_81_length_165907_cov_6.524706_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME130774 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900545585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_provirus.81 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11139857 SAMEA13537887 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738235. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537887 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 8.95043 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 64 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_1135_length_43196_cov_5.117535 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6774193548387096 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_1135_length_43196_cov_5.117535 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738210_provirus.191 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11139859 SAMEA13537889 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738235. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537889 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 28.3618 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_2099_length_27804_cov_16.870740 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_2099_length_27804_cov_16.870740 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.227 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139860 SAMEA13537890 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738235. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537890 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 12.2394 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_518_length_67784_cov_7.376963 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_518_length_67784_cov_7.376963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738238_provirus.89 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139861 SAMEA13537891 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738235. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537891 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 77.3914 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 430 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_718_length_56525_cov_45.702151 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_718_length_56525_cov_45.702151 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738206_virus.525 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139862 SAMEA13537892 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738236. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537892 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 63.783 MAG coverage software Reads (ERR7738236) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561643) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_F_18_1212__NODE_19_length_180082_cov_35.602483_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585635 sample name Hadza_MoBio_hadza-I-L_F_18_1212__NODE_19_length_180082_cov_35.602483_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738236_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139863 SAMEA13537893 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738236. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537893 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 453.25 MAG coverage software Reads (ERR7738236) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561643) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 665 Submitter Id Hadza_MoBio_hadza-I-L_F_18_1212__NODE_231_length_40837_cov_257.005079 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585635 sample name Hadza_MoBio_hadza-I-L_F_18_1212__NODE_231_length_40837_cov_257.005079 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738210_provirus.701 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139864 SAMEA13537894 340016 uncultured virus This sample represents an uncultured Inovirus sp. provirus assembled from ERR7738237. BACPHLIP temperate score 0.11996874984972046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537894 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 47.2613 MAG coverage software Reads (ERR7738237) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560661) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_C_1_1708__NODE_20457_length_4035_cov_27.215766_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585951 sample name Hadza_MoBio_hadza-E-H_C_1_1708__NODE_20457_length_4035_cov_27.215766_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900545495;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738237_provirus.20457 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae; Inovirus; unclassified Inovirus; Inovirus sp. virus enrichment approach none ERS11139865 SAMEA13537895 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738237. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537895 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 8.28713 MAG coverage software Reads (ERR7738237) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560661) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_C_1_1708__NODE_633_length_63739_cov_4.483004_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585951 sample name Hadza_MoBio_hadza-E-H_C_1_1708__NODE_633_length_63739_cov_4.483004_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738237_provirus.633 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139866 SAMEA13537896 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738237. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537896 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 9.25239 MAG coverage software Reads (ERR7738237) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560661) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_C_1_1708__NODE_1036_length_43754_cov_5.176981 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.43478260869565216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585951 sample name Hadza_MoBio_hadza-E-H_C_1_1708__NODE_1036_length_43754_cov_5.176981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738237_virus.1036 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139868 SAMEA13537898 2133760 Siphoviridae environmental samples This sample represents an uncultured Cecivirus virus assembled from ERR7738237. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537898 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 55.6872 MAG coverage software Reads (ERR7738237) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560661) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_C_1_1708__NODE_2730_length_19651_cov_34.311485 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585951 sample name Hadza_MoBio_hadza-E-H_C_1_1708__NODE_2730_length_19651_cov_34.311485 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000862 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus fermentum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738237_virus.2730 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cecivirus virus enrichment approach none ERS11139869 SAMEA13537899 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738237. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537899 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 41.7239 MAG coverage software Reads (ERR7738237) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560661) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_C_1_1708__NODE_3776_length_15200_cov_24.000860 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585951 sample name Hadza_MoBio_hadza-E-H_C_1_1708__NODE_3776_length_15200_cov_24.000860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745613_virus.4024 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139870 SAMEA13537900 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738237. BACPHLIP temperate score 0.17747797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537900 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 9.48821 MAG coverage software Reads (ERR7738237) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560661) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_C_1_1708__NODE_729_length_57588_cov_5.379423 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.35294117647058826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585951 sample name Hadza_MoBio_hadza-E-H_C_1_1708__NODE_729_length_57588_cov_5.379423 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745433_bin.145 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738237_virus.729 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139871 SAMEA13537901 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738238. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537901 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 267.777 MAG coverage software Reads (ERR7738238) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560650) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-E-H_E_3_1720__NODE_170_length_80924_cov_132.589979_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.391304347826087 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585963 sample name Hadza_MoBio_hadza-E-H_E_3_1720__NODE_170_length_80924_cov_132.589979_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738238_provirus.170 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139872 SAMEA13537902 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738238. BACPHLIP temperate score 0.170090861558364 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537902 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 8.92359 MAG coverage software Reads (ERR7738238) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560650) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 206 Submitter Id Hadza_MoBio_hadza-E-H_E_3_1720__NODE_1210_length_20646_cov_4.890126 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585963 sample name Hadza_MoBio_hadza-E-H_E_3_1720__NODE_1210_length_20646_cov_4.890126 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000518 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor;s__Flavonifractor plautii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738238_virus.1210 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139874 SAMEA13537904 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738239. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537904 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 34.951 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_16_length_356441_cov_20.999259_2 Viral contig found in MAG ERR7738239_bin.83 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8958333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_16_length_356441_cov_20.999259_2 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_virus.1011 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139875 SAMEA13537905 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738239. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537905 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 57.4467 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 303 Number of CRISPR spacer hits supporting host taxonomy 186 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_53_length_190370_cov_34.189503_1 Viral contig found in MAG ERR7738239_bin.125 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7878787878787878 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_53_length_190370_cov_34.189503_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253237 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465;s__CAG-465 sp000433755 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_provirus.53 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139876 SAMEA13537906 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738239. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537906 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 256.116 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 69 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_1126_length_40298_cov_155.593620 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_1126_length_40298_cov_155.593620 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.1126 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139877 SAMEA13537907 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus virus assembled from ERR7738239. BACPHLIP temperate score 0.6 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537907 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 45.6279 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 97 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_1494_length_34132_cov_25.381912 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_1494_length_34132_cov_25.381912 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.1494 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11139878 SAMEA13537908 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738239. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537908 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 10.0937 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_195_length_104037_cov_5.940583 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.9078947368421052 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_195_length_104037_cov_5.940583 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.368 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139879 SAMEA13537909 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738239. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537909 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 13.7322 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 153 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_2809_length_23069_cov_8.105515 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_2809_length_23069_cov_8.105515 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0261276 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139880 SAMEA13537910 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738239. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537910 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 11.1791 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 541 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_540_length_59280_cov_6.605392 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_540_length_59280_cov_6.605392 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.540 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139882 SAMEA13537912 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738240. BACPHLIP temperate score 0.6529216648425764 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537912 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 8.95769 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1999_length_30500_cov_5.293462_1 Viral contig found in MAG ERR7738240_bin.207 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1999_length_30500_cov_5.293462_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747083_virus.1678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139883 SAMEA13537913 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738240. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537913 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 14.1847 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_412_length_80538_cov_8.493730_1 Viral contig found in MAG ERR7738240_bin.101 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_412_length_80538_cov_8.493730_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0297475 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139884 SAMEA13537914 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738240. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537914 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 9.63632 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 353 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1056_length_45926_cov_5.713712 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1056_length_45926_cov_5.713712 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745743_provirus.1046 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139885 SAMEA13537915 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738240. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537915 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 44.8645 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1370_length_39233_cov_26.873685 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1370_length_39233_cov_26.873685 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738240_virus.1370 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139886 SAMEA13537916 2133760 Siphoviridae environmental samples This sample represents an uncultured Teubervirus virus assembled from ERR7738240. BACPHLIP temperate score 0.0922356828193833 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537916 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 363.928 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1690_length_34020_cov_218.473853 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_1690_length_34020_cov_218.473853 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Teubervirus virus enrichment approach none ERS11139888 SAMEA13537919 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738240. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537919 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 12.4644 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_330_length_91500_cov_7.361988 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.5957446808510638 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_330_length_91500_cov_7.361988 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139889 SAMEA13537920 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738240. BACPHLIP temperate score 0.18368843659633977 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537920 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 33.0459 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_5703_length_13665_cov_19.939965 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_5703_length_13665_cov_19.939965 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.7471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139890 SAMEA13537921 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738240. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537921 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 20.3828 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_786_length_55899_cov_12.312726 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_786_length_55899_cov_12.312726 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738240_virus.786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139891 SAMEA13537922 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738241. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537922 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 11.8582 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_1866_length_27837_cov_6.974099_1 Viral contig found in MAG ERR7738241_bin.57 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_1866_length_27837_cov_6.974099_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738250_provirus.6 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139892 SAMEA13537923 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738241. BACPHLIP temperate score 0.5298458149779736 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537923 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 12.3078 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_507_length_72502_cov_7.322651_1 Viral contig found in MAG ERR7738241_bin.205 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_507_length_72502_cov_7.322651_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738241_provirus.507 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139893 SAMEA13537924 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738241. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537924 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 43.1956 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 166 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_1014_length_45685_cov_26.718887 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_1014_length_45685_cov_26.718887 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139894 SAMEA13537925 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738241. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537925 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 14.299 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 267 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_1197_length_39700_cov_8.526184 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7037037037037037 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_1197_length_39700_cov_8.526184 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.1677 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139895 SAMEA13537926 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738241. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537926 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 11.7823 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_205_length_122221_cov_7.175825 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_205_length_122221_cov_7.175825 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738605_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139897 SAMEA13537928 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738241. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537928 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 14.6372 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_397_length_82689_cov_8.787973 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_397_length_82689_cov_8.787973 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_provirus.322 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139898 SAMEA13537929 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738241. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537929 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 70.1597 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_730_length_57624_cov_43.754670 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_730_length_57624_cov_43.754670 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738241_virus.730 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139899 SAMEA13537930 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738242. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537930 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 26.8076 MAG coverage software Reads (ERR7738242) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561200) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_B_14_1607__NODE_273_length_72940_cov_17.138754_1 Viral contig found in MAG ERR7738242_bin.118 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585856 sample name Hadza_MoBio_hadza-A-D_B_14_1607__NODE_273_length_72940_cov_17.138754_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738221_virus.807 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139900 SAMEA13537931 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738242. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537931 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 74.63 MAG coverage software Reads (ERR7738242) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561200) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-A-D_B_14_1607__NODE_85_length_125326_cov_45.458910_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585856 sample name Hadza_MoBio_hadza-A-D_B_14_1607__NODE_85_length_125326_cov_45.458910_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_provirus.1065 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139901 SAMEA13537932 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738242. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537932 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 7.26582 MAG coverage software Reads (ERR7738242) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561200) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 205 Submitter Id Hadza_MoBio_hadza-A-D_B_14_1607__NODE_1297_length_31322_cov_4.274316 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585856 sample name Hadza_MoBio_hadza-A-D_B_14_1607__NODE_1297_length_31322_cov_4.274316 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1457 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139903 SAMEA13537934 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738242. BACPHLIP temperate score 0.01358752575482346 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537934 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 17.0749 MAG coverage software Reads (ERR7738242) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561200) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_14_1607__NODE_2921_length_18971_cov_10.421827 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585856 sample name Hadza_MoBio_hadza-A-D_B_14_1607__NODE_2921_length_18971_cov_10.421827 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139904 SAMEA13537935 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738242. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537935 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 11.4512 MAG coverage software Reads (ERR7738242) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561200) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 72 Number of CRISPR spacer hits supporting host taxonomy 282 Submitter Id Hadza_MoBio_hadza-A-D_B_14_1607__NODE_796_length_41540_cov_6.855823 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585856 sample name Hadza_MoBio_hadza-A-D_B_14_1607__NODE_796_length_41540_cov_6.855823 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139905 SAMEA13537936 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738243. BACPHLIP temperate score 0.02597739359623315 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537936 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 31.1708 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_217_length_109696_cov_19.575448_1 Viral contig found in MAG ERR7738243_bin.140 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_217_length_109696_cov_19.575448_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257483 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__UBA644;g__UBA644;s__UBA644 sp900547165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_provirus.217 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139906 SAMEA13537937 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738243. BACPHLIP temperate score 0.11976362772252648 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537937 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 11.9548 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_55_length_190851_cov_7.429838_1 Viral contig found in MAG ERR7738243_bin.14 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_55_length_190851_cov_7.429838_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139907 SAMEA13537938 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738243. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537938 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 27.907 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_1171_length_39547_cov_17.413327 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7837837837837838 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_1171_length_39547_cov_17.413327 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.1171 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139908 SAMEA13537939 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738243. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537939 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 24.1402 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_1792_length_29395_cov_15.146531 Viral contig found in MAG ERR7738243_bin.10 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_1792_length_29395_cov_15.146531 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.1792 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139909 SAMEA13537940 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade sp. virus assembled from ERR7738243. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537940 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 1013.19 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_239_length_104652_cov_621.357896 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6274509803921569 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_239_length_104652_cov_621.357896 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.239 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; UAG-readthrough crAss clade sp. virus enrichment approach none ERS11139911 SAMEA13537942 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738243. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537942 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 27.1668 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_623_length_61104_cov_16.692792 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_623_length_61104_cov_16.692792 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738148_bin.20 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A;s__Selenomonas_A sp900769615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.623 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139912 SAMEA13537943 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738243. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537943 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 28.2258 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_928_length_46439_cov_17.610047 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_928_length_46439_cov_17.610047 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.928 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139913 SAMEA13537944 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738244. BACPHLIP temperate score 0.6799559471365638 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537944 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 112.312 MAG coverage software Reads (ERR7738244) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561180) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-A-D_B_24_1613__NODE_232_length_72256_cov_68.528131_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585862 sample name Hadza_MoBio_hadza-A-D_B_24_1613__NODE_232_length_72256_cov_68.528131_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.72 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139914 SAMEA13537945 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738244. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537945 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 14.0342 MAG coverage software Reads (ERR7738244) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561180) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 157 Submitter Id Hadza_MoBio_hadza-A-D_B_24_1613__NODE_80_length_115202_cov_8.274467_1 Viral contig found in MAG ERR7738244_bin.37 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585862 sample name Hadza_MoBio_hadza-A-D_B_24_1613__NODE_80_length_115202_cov_8.274467_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11139915 SAMEA13537946 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738244. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537946 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 36.8235 MAG coverage software Reads (ERR7738244) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561180) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 223 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_B_24_1613__NODE_117_length_98451_cov_22.556255 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9696969696969696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585862 sample name Hadza_MoBio_hadza-A-D_B_24_1613__NODE_117_length_98451_cov_22.556255 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_virus.117 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139917 SAMEA13537948 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738244. BACPHLIP temperate score 0.10825856553536624 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537948 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 10.0617 MAG coverage software Reads (ERR7738244) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561180) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-A-D_B_24_1613__NODE_493_length_49989_cov_6.014145 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585862 sample name Hadza_MoBio_hadza-A-D_B_24_1613__NODE_493_length_49989_cov_6.014145 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139918 SAMEA13537949 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738244. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537949 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 8.56614 MAG coverage software Reads (ERR7738244) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561180) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_B_24_1613__NODE_896_length_34820_cov_4.997784 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585862 sample name Hadza_MoBio_hadza-A-D_B_24_1613__NODE_896_length_34820_cov_4.997784 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000493 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea;s__Dorea formicigenerans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.2480 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139919 SAMEA13537950 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738245. BACPHLIP temperate score 0.4125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537950 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 17.0006 MAG coverage software Reads (ERR7738245) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561113) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 202 Submitter Id Hadza_MoBio_hadza-A-D_B_21_1589__NODE_24_length_315731_cov_10.283766_1 Viral contig found in MAG ERR7738245_bin.204 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; HMM-based (lower-bound) completeness score 67.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585838 sample name Hadza_MoBio_hadza-A-D_B_21_1589__NODE_24_length_315731_cov_10.283766_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745434_provirus.74 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139920 SAMEA13537951 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738245. BACPHLIP temperate score 5.538234328848e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537951 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 62.1804 MAG coverage software Reads (ERR7738245) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561113) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_hadza-A-D_B_21_1589__NODE_5_length_495339_cov_75.710168_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585838 sample name Hadza_MoBio_hadza-A-D_B_21_1589__NODE_5_length_495339_cov_75.710168_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139921 SAMEA13537952 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738245. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537952 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 12.6632 MAG coverage software Reads (ERR7738245) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561113) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 82 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_B_21_1589__NODE_802_length_52937_cov_7.611880_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8928571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585838 sample name Hadza_MoBio_hadza-A-D_B_21_1589__NODE_802_length_52937_cov_7.611880_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.945 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139922 SAMEA13537953 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738245. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537953 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 18.411 MAG coverage software Reads (ERR7738245) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561113) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_B_21_1589__NODE_1660_length_31205_cov_11.253341 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585838 sample name Hadza_MoBio_hadza-A-D_B_21_1589__NODE_1660_length_31205_cov_11.253341 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745908_bin.152 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433;s__CAG-433 sp000433675 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_virus.695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139923 SAMEA13537954 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738245. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537954 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 6.95703 MAG coverage software Reads (ERR7738245) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561113) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_21_1589__NODE_2204_length_24820_cov_4.086368 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585838 sample name Hadza_MoBio_hadza-A-D_B_21_1589__NODE_2204_length_24820_cov_4.086368 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738591_bin.256 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UMGS1603;s__UMGS1603 sp900553265 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_virus.2204 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139924 SAMEA13537955 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738245. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537955 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 20.2987 MAG coverage software Reads (ERR7738245) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561113) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_B_21_1589__NODE_3841_length_15144_cov_12.051245 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585838 sample name Hadza_MoBio_hadza-A-D_B_21_1589__NODE_3841_length_15144_cov_12.051245 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745613_bin.13 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;s__Marvinbryantia sp014385005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.3347 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11139926 SAMEA13537957 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738246. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537957 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 59.0912 MAG coverage software Reads (ERR7738246) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-I-L_N_24_1344__NODE_45_length_153820_cov_29.305829_1 Viral contig found in MAG ERR7738246_bin.20 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7837837837837838 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_N_24_1344__NODE_45_length_153820_cov_29.305829_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738173_virus.612 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139927 SAMEA13537958 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738246. BACPHLIP temperate score 0.6649779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537958 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 1611.4 MAG coverage software Reads (ERR7738246) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 191 Submitter Id Hadza_MoBio_hadza-I-L_N_24_1344__NODE_270_length_60775_cov_781.263600 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_N_24_1344__NODE_270_length_60775_cov_781.263600 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0338166 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139928 SAMEA13537959 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738246. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537959 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 21.9285 MAG coverage software Reads (ERR7738246) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-I-L_N_24_1344__NODE_610_length_31689_cov_10.056086 Viral contig found in MAG ERR7738246_bin.12 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6071428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_N_24_1344__NODE_610_length_31689_cov_10.056086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738173_virus.803 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139929 SAMEA13537960 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7738247. BACPHLIP temperate score 0.00379359296842034 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537960 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 65.8218 MAG coverage software Reads (ERR7738247) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560527) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_M_22_1922__NODE_156_length_147936_cov_39.052645_1 Viral contig found in MAG ERR7738247_bin.79 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586065 sample name Hadza_MoBio_hadza-E-H_M_22_1922__NODE_156_length_147936_cov_39.052645_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738493_provirus.374 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11139930 SAMEA13537961 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738247. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537961 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 122.037 MAG coverage software Reads (ERR7738247) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560527) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 178 Submitter Id Hadza_MoBio_hadza-E-H_M_22_1922__NODE_592_length_72372_cov_84.149263_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586065 sample name Hadza_MoBio_hadza-E-H_M_22_1922__NODE_592_length_72372_cov_84.149263_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253237 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465;s__CAG-465 sp000433755 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738247_provirus.592 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139932 SAMEA13537963 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738247. BACPHLIP temperate score 0.2498898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537963 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 930.612 MAG coverage software Reads (ERR7738247) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560527) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 449 Submitter Id Hadza_MoBio_hadza-E-H_M_22_1922__NODE_1722_length_35270_cov_540.975251 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586065 sample name Hadza_MoBio_hadza-E-H_M_22_1922__NODE_1722_length_35270_cov_540.975251 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738273_bin.125 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__WG-1;s__WG-1 sp900539665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738247_virus.1722 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139933 SAMEA13537964 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738247. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537964 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 14.5984 MAG coverage software Reads (ERR7738247) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560527) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_M_22_1922__NODE_2336_length_27329_cov_8.575627 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586065 sample name Hadza_MoBio_hadza-E-H_M_22_1922__NODE_2336_length_27329_cov_8.575627 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.2569 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139934 SAMEA13537965 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738247. BACPHLIP temperate score 0.03480176211453744 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537965 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 52.7885 MAG coverage software Reads (ERR7738247) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560527) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_M_22_1922__NODE_634_length_69858_cov_31.011966 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 62.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586065 sample name Hadza_MoBio_hadza-E-H_M_22_1922__NODE_634_length_69858_cov_31.011966 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746111_bin.22 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738247_virus.634 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139935 SAMEA13537966 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738248. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537966 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 34.6932 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_1198_length_44389_cov_20.978674_1 Viral contig found in MAG ERR7738248_bin.149 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_1198_length_44389_cov_20.978674_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_provirus.1198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139936 SAMEA13537967 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738248. BACPHLIP temperate score 0.802477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537967 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 17.7236 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_2054_length_31731_cov_10.732672_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_2054_length_31731_cov_10.732672_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME108259 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900313215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_provirus.763 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139937 SAMEA13537968 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738248. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537968 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 13.478 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_718_length_60917_cov_8.211769_1 Viral contig found in MAG ERR7738248_bin.35 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_718_length_60917_cov_8.211769_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_provirus.718 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139938 SAMEA13537969 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738248. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537969 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 101.996 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 432 Number of CRISPR spacer hits supporting host taxonomy 156 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_1382_length_40906_cov_68.131941 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_1382_length_40906_cov_68.131941 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0341270 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139940 SAMEA13537971 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738248. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537971 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 28.7788 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 827 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_2022_length_32015_cov_16.642714 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_2022_length_32015_cov_16.642714 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745382_virus.1416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139941 SAMEA13537972 2133760 Siphoviridae environmental samples This sample represents an uncultured Streptococcus phage Javan351 virus assembled from ERR7738248. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537972 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 7.63451 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_2661_length_26367_cov_4.529479 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_2661_length_26367_cov_4.529479 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME269197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615;s__KLE1615 sp900066985 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_virus.1149 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Streptococcus phage Javan351 virus enrichment approach none ERS11139942 SAMEA13537973 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738248. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537973 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 30.9647 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 193 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_572_length_70189_cov_19.039808 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_572_length_70189_cov_19.039808 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_virus.572 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11139943 SAMEA13537974 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738248. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537974 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 9.41285 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 125 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_948_length_51261_cov_5.658917 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_948_length_51261_cov_5.658917 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139944 SAMEA13537975 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738249. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537975 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 13.5427 MAG coverage software Reads (ERR7738249) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559438) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_D_23_2656__NODE_480_length_64522_cov_8.288665_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586357 sample name Hadza_MoBio_hadza-I-L_D_23_2656__NODE_480_length_64522_cov_8.288665_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME007974 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp003516765 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738249_provirus.480 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139946 SAMEA13537977 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738249. BACPHLIP temperate score 0.03884348183251045 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537977 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 9.25674 MAG coverage software Reads (ERR7738249) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559438) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_D_23_2656__NODE_1433_length_29468_cov_5.391719 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586357 sample name Hadza_MoBio_hadza-I-L_D_23_2656__NODE_1433_length_29468_cov_5.391719 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_provirus.49 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139947 SAMEA13537978 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738249. BACPHLIP temperate score 0.24573785867882625 ENA-FIRST-PUBLIC 2022-12-27T00:31:16Z ENA-LAST-UPDATE 2022-12-27T00:31:16Z External Id SAMEA13537978 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 66.256 MAG coverage software Reads (ERR7738249) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559438) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Submitter Id Hadza_MoBio_hadza-I-L_D_23_2656__NODE_2352_length_18984_cov_39.528514 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; HMM-based (lower-bound) completeness score 58.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586357 sample name Hadza_MoBio_hadza-I-L_D_23_2656__NODE_2352_length_18984_cov_39.528514 scientific_name uncultured podovirus sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738249_virus.2352 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae ERS11139948 SAMEA13537979 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738249. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537979 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 554.304 MAG coverage software Reads (ERR7738249) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559438) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 141 Submitter Id Hadza_MoBio_hadza-I-L_D_23_2656__NODE_363_length_76388_cov_330.993802 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4827586206896552 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586357 sample name Hadza_MoBio_hadza-I-L_D_23_2656__NODE_363_length_76388_cov_330.993802 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745420_virus.131 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139949 SAMEA13537980 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738249. BACPHLIP temperate score 0.08631662166094103 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537980 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 84.6176 MAG coverage software Reads (ERR7738249) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559438) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-I-L_D_23_2656__NODE_555_length_59486_cov_53.796697 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586357 sample name Hadza_MoBio_hadza-I-L_D_23_2656__NODE_555_length_59486_cov_53.796697 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.703 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139950 SAMEA13537981 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738249. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537981 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 19.7353 MAG coverage software Reads (ERR7738249) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559438) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 116 Submitter Id Hadza_MoBio_hadza-I-L_D_23_2656__NODE_796_length_46489_cov_11.815436 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586357 sample name Hadza_MoBio_hadza-I-L_D_23_2656__NODE_796_length_46489_cov_11.815436 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_virus.471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139951 SAMEA13537982 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738250. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537982 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 22.6643 MAG coverage software Reads (ERR7738250) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_C_6_1832__NODE_209_length_85802_cov_11.447711_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586028 sample name Hadza_MoBio_hadza-E-H_C_6_1832__NODE_209_length_85802_cov_11.447711_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.160 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139952 SAMEA13537983 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738250. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537983 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 24.2813 MAG coverage software Reads (ERR7738250) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_C_6_1832__NODE_6_length_532051_cov_14.074169_1 Viral contig found in MAG ERR7738250_bin.50 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586028 sample name Hadza_MoBio_hadza-E-H_C_6_1832__NODE_6_length_532051_cov_14.074169_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738250_provirus.6 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139953 SAMEA13537984 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus virus assembled from ERR7738250. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537984 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 22.1038 MAG coverage software Reads (ERR7738250) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 255 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-E-H_C_6_1832__NODE_1538_length_23438_cov_12.210308 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586028 sample name Hadza_MoBio_hadza-E-H_C_6_1832__NODE_1538_length_23438_cov_12.210308 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738250_virus.1538 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11139955 SAMEA13537986 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade sp. virus assembled from ERR7738250. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537986 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 84.7252 MAG coverage software Reads (ERR7738250) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_C_6_1832__NODE_361_length_61901_cov_47.919497 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7049180327868853 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586028 sample name Hadza_MoBio_hadza-E-H_C_6_1832__NODE_361_length_61901_cov_47.919497 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; UAG-readthrough crAss clade sp. virus enrichment approach none ERS11139956 SAMEA13537987 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738250. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537987 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 49.8517 MAG coverage software Reads (ERR7738250) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 64 Submitter Id Hadza_MoBio_hadza-E-H_C_6_1832__NODE_598_length_43555_cov_28.388242 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586028 sample name Hadza_MoBio_hadza-E-H_C_6_1832__NODE_598_length_43555_cov_28.388242 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745823_bin.49 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001;s__SFJ001 sp004555865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738250_virus.598 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139957 SAMEA13537988 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738250. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537988 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 15.605 MAG coverage software Reads (ERR7738250) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 79 Submitter Id Hadza_MoBio_hadza-E-H_C_6_1832__NODE_908_length_33708_cov_8.521662 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586028 sample name Hadza_MoBio_hadza-E-H_C_6_1832__NODE_908_length_33708_cov_8.521662 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738250_virus.908 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139958 SAMEA13537989 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738251. BACPHLIP temperate score 0.1786756314816957 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537989 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 11.3472 MAG coverage software Reads (ERR7738251) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 88 Number of CRISPR spacer hits supporting host taxonomy 100 Submitter Id Hadza_MoBio_hadza-A-D_L_23_1525__NODE_223_length_101696_cov_6.683662_1 Viral contig found in MAG ERR7738251_bin.222 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_MoBio_hadza-A-D_L_23_1525__NODE_223_length_101696_cov_6.683662_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139959 SAMEA13537990 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe provirus assembled from ERR7738251. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537990 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 13.7033 MAG coverage software Reads (ERR7738251) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 549 Number of CRISPR spacer hits supporting host taxonomy 1382 Submitter Id Hadza_MoBio_hadza-A-D_L_23_1525__NODE_633_length_54991_cov_8.382635_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5490196078431373 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_MoBio_hadza-A-D_L_23_1525__NODE_633_length_54991_cov_8.382635_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11139961 SAMEA13537992 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738251. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537992 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 16.5732 MAG coverage software Reads (ERR7738251) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_L_23_1525__NODE_2241_length_24515_cov_10.259105 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_MoBio_hadza-A-D_L_23_1525__NODE_2241_length_24515_cov_10.259105 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.478 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139962 SAMEA13537993 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738251. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537993 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 13.2033 MAG coverage software Reads (ERR7738251) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_L_23_1525__NODE_37_length_234413_cov_8.073019 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_MoBio_hadza-A-D_L_23_1525__NODE_37_length_234413_cov_8.073019 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_virus.26 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139963 SAMEA13537994 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738251. BACPHLIP temperate score 0.03518635291109225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537994 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 8.68118 MAG coverage software Reads (ERR7738251) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_L_23_1525__NODE_986_length_42688_cov_5.063763 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_MoBio_hadza-A-D_L_23_1525__NODE_986_length_42688_cov_5.063763 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.780 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139964 SAMEA13537995 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738252. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537995 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 39.7151 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_222_length_109479_cov_24.366657_1 Viral contig found in MAG ERR7738252_bin.235 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_222_length_109479_cov_24.366657_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745743_provirus.819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139965 SAMEA13537996 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738252. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537996 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 74.104 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 144 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_487_length_72581_cov_46.443713_1 Viral contig found in MAG ERR7738252_bin.183 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_487_length_72581_cov_46.443713_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME116282 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873;s__CAG-873 sp001701165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_provirus.487 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139966 SAMEA13537997 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738252. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537997 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 52.1053 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_1003_length_45916_cov_30.539541 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_1003_length_45916_cov_30.539541 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.1551 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139967 SAMEA13537998 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738252. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537998 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 9.38227 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 452 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_1184_length_40569_cov_5.590882 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; HMM-based (lower-bound) completeness score 79.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_1184_length_40569_cov_5.590882 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270564 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.1184 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139969 SAMEA13538000 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738252. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538000 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 8.25301 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_1561_length_33481_cov_4.628248 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_1561_length_33481_cov_4.628248 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.1561 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139970 SAMEA13538001 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738252. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538001 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 10.2322 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_2256_length_25264_cov_6.088538 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_2256_length_25264_cov_6.088538 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.2256 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139971 SAMEA13538002 2133760 Siphoviridae environmental samples This sample represents an uncultured Erysipelothrix phage SE-1 virus assembled from ERR7738252. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538002 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 71.5769 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_3319_length_18758_cov_42.500027 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_3319_length_18758_cov_42.500027 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738447_bin.86 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.572 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Erysipelothrix phage SE-1 virus enrichment approach none ERS11139972 SAMEA13538003 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738252. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538003 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 78.0537 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_410_length_81489_cov_44.950671 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6451612903225806 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_410_length_81489_cov_44.950671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.856 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139973 SAMEA13538004 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738252. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538004 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 209.366 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_538_length_68012_cov_123.522794 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_538_length_68012_cov_123.522794 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.538 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139975 SAMEA13538006 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738252. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538006 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 29.0198 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_861_length_51298_cov_18.015189 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4634146341463415 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_861_length_51298_cov_18.015189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.1369 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139976 SAMEA13538007 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738253. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538007 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 82.3195 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_14_length_377029_cov_47.716370_1 Viral contig found in MAG ERR7738253_bin.105 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_14_length_377029_cov_47.716370_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.14 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139977 SAMEA13538008 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738253. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538008 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 7.96901 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_2903_length_27517_cov_4.283673_1 Viral contig found in MAG ERR7738253_bin.233 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_2903_length_27517_cov_4.283673_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746345_bin.279 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA791;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.2903 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11139978 SAMEA13538009 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738253. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538009 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 26.4722 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_808_length_73612_cov_15.486245_1 Viral contig found in MAG ERR7738253_bin.170 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 63.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_808_length_73612_cov_15.486245_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.808 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139979 SAMEA13538010 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738253. BACPHLIP temperate score 0.6049559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538010 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 58.7813 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1103_length_59490_cov_34.418477 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1103_length_59490_cov_34.418477 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738152_bin.166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900546445 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.1428 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11139980 SAMEA13538011 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 0.07747797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538011 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 18.2276 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1300_length_53174_cov_10.513984 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1300_length_53174_cov_10.513984 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.1300 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139981 SAMEA13538012 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538012 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 10 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1551_length_46144_cov_5.746435 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1551_length_46144_cov_5.746435 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.1551 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139982 SAMEA13538013 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538013 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 63.9895 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1647_length_43994_cov_36.614295 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1647_length_43994_cov_36.614295 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.328 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1750;g__UBA7102;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_virus.1950 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139984 SAMEA13538015 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738253. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538015 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 14.6718 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 188 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_18900_length_4735_cov_8.864105 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_18900_length_4735_cov_8.864105 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.27072 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11139985 SAMEA13538016 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7738253. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538016 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 7.69039 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 111 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_2104_length_36247_cov_4.267321 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_2104_length_36247_cov_4.267321 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.2104 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11139986 SAMEA13538017 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 0.12738393726507272 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538017 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 12.0265 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_2514_length_30972_cov_7.385111 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_2514_length_30972_cov_7.385111 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.2514 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139987 SAMEA13538018 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538018 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 30.1828 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_3162_length_25480_cov_18.078022 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_3162_length_25480_cov_18.078022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0256920 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139988 SAMEA13538019 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 0.7449339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538019 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 10.7678 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_3822_length_21432_cov_6.075626 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_3822_length_21432_cov_6.075626 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.730 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139990 SAMEA13538021 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738253. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538021 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 95.7493 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_583_length_91495_cov_54.057593 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_583_length_91495_cov_54.057593 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.161 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900545925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11139991 SAMEA13538022 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738253. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538022 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 29.5519 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_940_length_66128_cov_17.005087 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_940_length_66128_cov_17.005087 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091217 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973;s__UMGS973 sp900547295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.940 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139992 SAMEA13538023 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738254. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538023 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 34.5885 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_334_length_69313_cov_20.654818_1 Viral contig found in MAG ERR7738254_bin.109 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_334_length_69313_cov_20.654818_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_provirus.334 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139993 SAMEA13538024 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus provirus assembled from ERR7738254. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538024 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 12.6609 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_917_length_37406_cov_7.396876_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_917_length_37406_cov_7.396876_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME043942 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103;s__CAG-103 sp900317855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_provirus.917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11139994 SAMEA13538025 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738254. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538025 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 16.0851 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 142 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_128_length_113107_cov_9.699133 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_128_length_113107_cov_9.699133 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738616_bin.92 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745398_virus.207 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139995 SAMEA13538026 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738254. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538026 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 9.43186 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_1536_length_26480_cov_5.351968 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_1536_length_26480_cov_5.351968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139996 SAMEA13538027 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738254. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538027 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 7.50862 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_1844_length_23411_cov_4.182009 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_1844_length_23411_cov_4.182009 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_virus.1811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139998 SAMEA13538029 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738254. BACPHLIP temperate score 0.17747797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538029 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 8.09539 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_363_length_66549_cov_4.518700 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_363_length_66549_cov_4.518700 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738147_virus.102 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139999 SAMEA13538030 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738254. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538030 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 36.5925 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_477_length_56999_cov_21.774323 Viral contig found in MAG ERR7738254_bin.109 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 84.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_477_length_56999_cov_21.774323 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.879 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140000 SAMEA13538031 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738254. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538031 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 9.60557 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 68 Number of CRISPR spacer hits supporting host taxonomy 102 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_567_length_51526_cov_5.660227 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_567_length_51526_cov_5.660227 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140001 SAMEA13538032 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738254. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538032 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 8.58021 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_723_length_44274_cov_4.894359 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_723_length_44274_cov_4.894359 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.2161 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140002 SAMEA13538033 336724 Myoviridae environmental samples This sample represents an uncultured Bdellovibrio phage phi1422 virus assembled from ERR7738254. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538033 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 60.7769 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_804_length_41302_cov_35.758108 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5357142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_804_length_41302_cov_35.758108 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.804 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Bdellovibrio phage phi1422 virus enrichment approach none ERS11140004 SAMEA13538035 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738256. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538035 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 14.6683 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 269 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_224_length_85233_cov_8.416036_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6071428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_224_length_85233_cov_8.416036_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738256_provirus.224 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140005 SAMEA13538036 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738256. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538036 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 10.8833 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_394_length_63499_cov_6.164612_1 Viral contig found in MAG ERR7738256_bin.50 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_394_length_63499_cov_6.164612_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738152_bin.166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900546445 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_provirus.273 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140006 SAMEA13538037 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738256. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538037 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 21.0167 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 316 Number of CRISPR spacer hits supporting host taxonomy 618 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_1025_length_35570_cov_12.083932 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6176470588235294 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_1025_length_35570_cov_12.083932 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.561 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140007 SAMEA13538038 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738256. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538038 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 15.5163 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_157_length_100743_cov_9.145372 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_157_length_100743_cov_9.145372 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_virus.132 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140008 SAMEA13538039 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738256. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538039 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 13.0951 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_221_length_85847_cov_7.343873 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.5405405405405406 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_221_length_85847_cov_7.343873 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_virus.64 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140009 SAMEA13538040 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738256. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538040 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 28.4596 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 218 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_445_length_58974_cov_16.222218 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_445_length_58974_cov_16.222218 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372372 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140010 SAMEA13538041 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738256. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538041 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 185.139 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 137 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_677_length_45625_cov_108.466936 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_677_length_45625_cov_108.466936 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139823 SAMEA13537853 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7738230. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537853 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 12.8593 MAG coverage software Reads (ERR7738230) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561839) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_I_8_1124__NODE_47_length_235658_cov_7.348971 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5573770491803278 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585548 sample name Hadza_MoBio_hadza-A-D_I_8_1124__NODE_47_length_235658_cov_7.348971 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738628_bin.233 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1394;s__UBA1394 sp900554975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_virus.47 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11139844 SAMEA13537874 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738233. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537874 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 11.0508 MAG coverage software Reads (ERR7738233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559747) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_P_8_2357__NODE_371_length_76818_cov_6.433627 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.41379310344827586 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586224 sample name Hadza_MoBio_hadza-I-L_P_8_2357__NODE_371_length_76818_cov_6.433627 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_provirus.192 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139852 SAMEA13537882 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738234. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537882 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 79.3513 MAG coverage software Reads (ERR7738234) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 279 Number of CRISPR spacer hits supporting host taxonomy 353 Submitter Id Hadza_MoBio_hadza-I-L_B_17_2661__NODE_618_length_63250_cov_45.872841 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586362 sample name Hadza_MoBio_hadza-I-L_B_17_2661__NODE_618_length_63250_cov_45.872841 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738575_bin.23 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-279;s__CAG-279 sp000437795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_virus.618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139858 SAMEA13537888 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738235. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537888 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 11.1874 MAG coverage software Reads (ERR7738235) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559615) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 169 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_J_12_2311__NODE_1463_length_36277_cov_6.371436 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; ITR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586183 sample name Hadza_MoBio_hadza-E-H_J_12_2311__NODE_1463_length_36277_cov_6.371436 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_provirus.739 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139867 SAMEA13537897 340016 uncultured virus This sample represents an uncultured Pseudomonas phage PPAT virus assembled from ERR7738237. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537897 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 162.964 MAG coverage software Reads (ERR7738237) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560661) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_C_1_1708__NODE_1392_length_33887_cov_93.635644 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585951 sample name Hadza_MoBio_hadza-E-H_C_1_1708__NODE_1392_length_33887_cov_93.635644 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745613_virus.1460 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Pseudomonas phage PPAT virus enrichment approach none ERS11139873 SAMEA13537903 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738238. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537903 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 8.48951 MAG coverage software Reads (ERR7738238) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560650) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_E_3_1720__NODE_4305_length_6869_cov_4.521790 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585963 sample name Hadza_MoBio_hadza-E-H_E_3_1720__NODE_4305_length_6869_cov_4.521790 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME089567 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp001556435 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738238_virus.4305 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139881 SAMEA13537911 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738239. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537911 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 14.7642 MAG coverage software Reads (ERR7738239) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562116) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-A-D_L_17_1528__NODE_751_length_49752_cov_8.438671 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_MoBio_hadza-A-D_L_17_1528__NODE_751_length_49752_cov_8.438671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_provirus.55 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11139887 SAMEA13537917 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7738240. BACPHLIP temperate score 0.1960214464596693 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537917 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 9.03402 MAG coverage software Reads (ERR7738240) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562259) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 126 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-A-D_P_17_1504__NODE_2136_length_28959_cov_5.174295 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7407407407407407 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585760 sample name Hadza_MoBio_hadza-A-D_P_17_1504__NODE_2136_length_28959_cov_5.174295 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_virus.231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11139896 SAMEA13537927 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738241. BACPHLIP temperate score 0.04719162995594714 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537927 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 18.6535 MAG coverage software Reads (ERR7738241) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_B_4_1602__NODE_2891_length_19166_cov_11.019540 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585851 sample name Hadza_MoBio_hadza-A-D_B_4_1602__NODE_2891_length_19166_cov_11.019540 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.770 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139902 SAMEA13537933 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738242. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537933 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 19.9133 MAG coverage software Reads (ERR7738242) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561200) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_B_14_1607__NODE_16_length_225184_cov_12.306001 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585856 sample name Hadza_MoBio_hadza-A-D_B_14_1607__NODE_16_length_225184_cov_12.306001 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738242_virus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139910 SAMEA13537941 2100421 uncultured Caudovirales phage This sample represents an uncultured Schitoviridae virus assembled from ERR7738243. BACPHLIP temperate score 0.11513032049760293 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537941 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 63.1392 MAG coverage software Reads (ERR7738243) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 331 Submitter Id Hadza_MoBio_hadza-I-L_F_1_2651__NODE_437_length_74939_cov_38.976063 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586354 sample name Hadza_MoBio_hadza-I-L_F_1_2651__NODE_437_length_74939_cov_38.976063 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.669 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Schitoviridae virus enrichment approach none ERS11139916 SAMEA13537947 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738244. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537947 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 9.87277 MAG coverage software Reads (ERR7738244) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561180) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 378 Submitter Id Hadza_MoBio_hadza-A-D_B_24_1613__NODE_336_length_60428_cov_5.836457 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585862 sample name Hadza_MoBio_hadza-A-D_B_24_1613__NODE_336_length_60428_cov_5.836457 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1064 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139925 SAMEA13537956 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738246. BACPHLIP temperate score 0.1674559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537956 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 94.7204 MAG coverage software Reads (ERR7738246) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-I-L_N_24_1344__NODE_125_length_98526_cov_43.958638_1 Viral contig found in MAG ERR7738246_bin.53 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585751 sample name Hadza_MoBio_hadza-I-L_N_24_1344__NODE_125_length_98526_cov_43.958638_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738246_provirus.125 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139931 SAMEA13537962 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 virus assembled from ERR7738247. BACPHLIP temperate score 7.8965839962564e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537962 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 53.1459 MAG coverage software Reads (ERR7738247) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560527) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Hadza_MoBio_hadza-E-H_M_22_1922__NODE_1269_length_44094_cov_30.641752 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586065 sample name Hadza_MoBio_hadza-E-H_M_22_1922__NODE_1269_length_44094_cov_30.641752 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738152_bin.166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900546445 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.1061 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11139939 SAMEA13537970 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738248. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537970 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:16Z INSDC last update 2022-12-27T00:31:16Z INSDC status public MAG coverage depth 10.0596 MAG coverage software Reads (ERR7738248) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567741) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 76 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_1669_length_35967_cov_6.107189 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_18_2379__NODE_1669_length_35967_cov_6.107189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_virus.288 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139945 SAMEA13537976 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738249. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537976 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 166.267 MAG coverage software Reads (ERR7738249) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559438) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 137 Submitter Id Hadza_MoBio_hadza-I-L_D_23_2656__NODE_1064_length_37340_cov_100.184446 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586357 sample name Hadza_MoBio_hadza-I-L_D_23_2656__NODE_1064_length_37340_cov_100.184446 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000448 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900066885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738249_virus.1064 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139954 SAMEA13537985 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738250. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537985 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 10.8884 MAG coverage software Reads (ERR7738250) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_C_6_1832__NODE_1889_length_19859_cov_5.767566 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586028 sample name Hadza_MoBio_hadza-E-H_C_6_1832__NODE_1889_length_19859_cov_5.767566 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0167695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139960 SAMEA13537991 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738251. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537991 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 13.6918 MAG coverage software Reads (ERR7738251) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-A-D_L_23_1525__NODE_106_length_141988_cov_8.218736 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 19 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_MoBio_hadza-A-D_L_23_1525__NODE_106_length_141988_cov_8.218736 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.214 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139968 SAMEA13537999 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738252. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13537999 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:20Z INSDC last update 2022-12-27T19:09:20Z INSDC status public MAG coverage depth 107.197 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_13_length_353189_cov_64.297458 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; ITR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 25 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.5045045045045045 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_13_length_353189_cov_64.297458 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.13 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11139974 SAMEA13538005 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738252. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538005 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 9.87534 MAG coverage software Reads (ERR7738252) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_F_1_1963__NODE_693_length_58260_cov_5.901243 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586094 sample name Hadza_MoBio_hadza-E-H_F_1_1963__NODE_693_length_58260_cov_5.901243 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738537_bin.54 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales_A;f__UBA1381;g__UBA4716;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.693 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139983 SAMEA13538014 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538014 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 55.3974 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 291 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1793_length_41053_cov_31.826825 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 64.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7407407407407407 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_1793_length_41053_cov_31.826825 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738253_bin.86 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;s__Ruminiclostridium_E sp900556525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.1793 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139989 SAMEA13538020 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738253. BACPHLIP temperate score 0.03243392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538020 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 10.9502 MAG coverage software Reads (ERR7738253) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561663) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_M_24_1194__NODE_4521_length_18306_cov_6.102858 Viral contig found in MAG ERR7738253_bin.233 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585617 sample name Hadza_MoBio_hadza-A-D_M_24_1194__NODE_4521_length_18306_cov_6.102858 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.430 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11139997 SAMEA13538028 336724 Myoviridae environmental samples This sample represents an uncultured Bcepmuvirus virus assembled from ERR7738254. BACPHLIP temperate score 0.22052497998750176 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538028 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 6.64779 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_2456_length_18917_cov_3.718206 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_2456_length_18917_cov_3.718206 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738545_provirus.156 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Bcepmuvirus virus enrichment approach none ERS11140003 SAMEA13538034 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738254. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538034 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 9.7743 MAG coverage software Reads (ERR7738254) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 159 Number of CRISPR spacer hits supporting host taxonomy 77 Submitter Id Hadza_MoBio_hadza-A-D_E_2_1148__NODE_967_length_36154_cov_5.341908 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585572 sample name Hadza_MoBio_hadza-A-D_E_2_1148__NODE_967_length_36154_cov_5.341908 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140011 SAMEA13538042 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738256. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538042 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 11.3749 MAG coverage software Reads (ERR7738256) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561283) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-I-L_N_11_1304__NODE_932_length_38110_cov_6.365551 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585719 sample name Hadza_MoBio_hadza-I-L_N_11_1304__NODE_932_length_38110_cov_6.365551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_virus.1811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140012 SAMEA13538043 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738257. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538043 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 232.167 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_393_length_62049_cov_146.322985_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_393_length_62049_cov_146.322985_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_provirus.266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140013 SAMEA13538044 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738257. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538044 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 37.1779 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 167 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_68_length_143002_cov_21.517453_1 Viral contig found in MAG ERR7738257_bin.145 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_68_length_143002_cov_21.517453_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738257_provirus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140014 SAMEA13538045 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738257. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538045 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 8.056 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_1153_length_33721_cov_4.363750 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_1153_length_33721_cov_4.363750 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738257_virus.1153 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140015 SAMEA13538046 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738257. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538046 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 15.3613 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_1547_length_27643_cov_8.998368 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_1547_length_27643_cov_8.998368 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.1765 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140016 SAMEA13538047 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738257. BACPHLIP temperate score 0.02856549932310539 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538047 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 11.3 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_2853_length_17698_cov_6.609897 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_2853_length_17698_cov_6.609897 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738257_virus.2853 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140017 SAMEA13538048 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738257. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538048 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 16.5107 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 175 Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_562_length_51887_cov_9.450704 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5161290322580645 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_562_length_51887_cov_9.450704 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738147_virus.298 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140018 SAMEA13538049 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738257. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538049 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 11.2758 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_78_length_135533_cov_6.272435 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_78_length_135533_cov_6.272435 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738257_virus.78 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140019 SAMEA13538050 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7738257. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538050 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 24.3993 MAG coverage software Reads (ERR7738257) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_M_18_1188__NODE_912_length_39395_cov_13.745307 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_MoBio_hadza-A-D_M_18_1188__NODE_912_length_39395_cov_13.745307 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738257_virus.912 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11140020 SAMEA13538051 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lugh provirus assembled from ERR7738258. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538051 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 16.1953 MAG coverage software Reads (ERR7738258) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567482) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_373_length_70877_cov_9.464336_1 Viral contig found in MAG ERR7738258_bin.69 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5357142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787405 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_373_length_70877_cov_9.464336_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738451_virus.1084 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lughvirus; Faecalibacterium virus Lugh virus enrichment approach none ERS11140021 SAMEA13538052 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738258. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538052 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 8.27121 MAG coverage software Reads (ERR7738258) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567482) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_1378_length_26344_cov_4.650969 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787405 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_1378_length_26344_cov_4.650969 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140022 SAMEA13538053 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738258. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538053 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 95.0822 MAG coverage software Reads (ERR7738258) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567482) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_299_length_79348_cov_55.942766 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.627906976744186 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787405 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_299_length_79348_cov_55.942766 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738551_provirus.252 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140023 SAMEA13538054 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738258. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538054 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 8.23463 MAG coverage software Reads (ERR7738258) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567482) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 264 Number of CRISPR spacer hits supporting host taxonomy 196 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_705_length_46338_cov_4.408919 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787405 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_705_length_46338_cov_4.408919 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0354261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140024 SAMEA13538055 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7738258. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538055 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 148.636 MAG coverage software Reads (ERR7738258) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567482) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_889_length_39187_cov_87.568346 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787405 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_5_THA1064JZ__NODE_889_length_39187_cov_87.568346 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_virus.1413 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11140025 SAMEA13538056 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7738259. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538056 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 93.2726 MAG coverage software Reads (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_M_13_1797__NODE_230_length_80833_cov_41.243140_1 Viral contig found in MAG ERR7738259_bin.161 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-17 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586006 sample name Hadza_MoBio_hadza-E-H_M_13_1797__NODE_230_length_80833_cov_41.243140_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_provirus.123 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11140026 SAMEA13538057 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lugh virus assembled from ERR7738259. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538057 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 12.9088 MAG coverage software Reads (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_M_13_1797__NODE_1337_length_28266_cov_4.864344 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-17 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586006 sample name Hadza_MoBio_hadza-E-H_M_13_1797__NODE_1337_length_28266_cov_4.864344 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737974_provirus.828 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lughvirus; Faecalibacterium virus Lugh virus enrichment approach none ERS11140027 SAMEA13538058 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738259. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538058 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 28.5751 MAG coverage software Reads (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_hadza-E-H_M_13_1797__NODE_251_length_76814_cov_12.953008 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-17 completeness approach CheckV; HMM-based (lower-bound) completeness score 80.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.3611111111111111 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586006 sample name Hadza_MoBio_hadza-E-H_M_13_1797__NODE_251_length_76814_cov_12.953008 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_virus.251 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140028 SAMEA13538059 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738259. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538059 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 100.832 MAG coverage software Reads (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 211 Submitter Id Hadza_MoBio_hadza-E-H_M_13_1797__NODE_458_length_55758_cov_47.532839 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-17 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586006 sample name Hadza_MoBio_hadza-E-H_M_13_1797__NODE_458_length_55758_cov_47.532839 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_virus.458 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140029 SAMEA13538060 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738259. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538060 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 19.4304 MAG coverage software Reads (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_M_13_1797__NODE_692_length_43825_cov_9.615182 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-17 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8484848484848485 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586006 sample name Hadza_MoBio_hadza-E-H_M_13_1797__NODE_692_length_43825_cov_9.615182 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_virus.692 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140030 SAMEA13538061 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738259. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538061 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 16.3113 MAG coverage software Reads (ERR7738259) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560362) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-E-H_M_13_1797__NODE_956_length_35728_cov_7.727553 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-17 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586006 sample name Hadza_MoBio_hadza-E-H_M_13_1797__NODE_956_length_35728_cov_7.727553 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738616_bin.92 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.1152 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140031 SAMEA13538062 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738260. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538062 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 70.386 MAG coverage software Reads (ERR7738260) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560003) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_H_1_1976__NODE_38_length_185058_cov_30.332337_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9016393442622952 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586100 sample name Hadza_MoBio_hadza-E-H_H_1_1976__NODE_38_length_185058_cov_30.332337_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738260_provirus.38 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11140032 SAMEA13538063 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738260. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538063 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 15.8527 MAG coverage software Reads (ERR7738260) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560003) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_H_1_1976__NODE_798_length_46181_cov_6.330058_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8292682926829268 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586100 sample name Hadza_MoBio_hadza-E-H_H_1_1976__NODE_798_length_46181_cov_6.330058_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142483 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus;s__Lacticaseibacillus paracasei vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738260_provirus.798 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140033 SAMEA13538064 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738260. BACPHLIP temperate score 0.26745594713656384 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538064 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 107.035 MAG coverage software Reads (ERR7738260) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560003) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 310 Submitter Id Hadza_MoBio_hadza-E-H_H_1_1976__NODE_1454_length_31319_cov_54.623776 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586100 sample name Hadza_MoBio_hadza-E-H_H_1_1976__NODE_1454_length_31319_cov_54.623776 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_provirus.1220 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140034 SAMEA13538065 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738260. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538065 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 14.6528 MAG coverage software Reads (ERR7738260) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560003) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-E-H_H_1_1976__NODE_2058_length_24230_cov_5.992589 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586100 sample name Hadza_MoBio_hadza-E-H_H_1_1976__NODE_2058_length_24230_cov_5.992589 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.3375 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140035 SAMEA13538066 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738260. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538066 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 152.968 MAG coverage software Reads (ERR7738260) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560003) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 298 Number of CRISPR spacer hits supporting host taxonomy 132 Submitter Id Hadza_MoBio_hadza-E-H_H_1_1976__NODE_330_length_74869_cov_74.703551 Viral contig found in MAG ERR7738260_bin.104 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586100 sample name Hadza_MoBio_hadza-E-H_H_1_1976__NODE_330_length_74869_cov_74.703551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140036 SAMEA13538067 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738260. BACPHLIP temperate score 0.03997797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538067 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 17.8455 MAG coverage software Reads (ERR7738260) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560003) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_H_1_1976__NODE_586_length_54907_cov_9.449188 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.47368421052631576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586100 sample name Hadza_MoBio_hadza-E-H_H_1_1976__NODE_586_length_54907_cov_9.449188 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738260_virus.586 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140037 SAMEA13538068 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738261. BACPHLIP temperate score 0.65 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538068 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 16.8312 MAG coverage software Reads (ERR7738261) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 61 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_I_23_1769__NODE_146_length_127636_cov_10.082111_1 Viral contig found in MAG ERR7738261_bin.159 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585991 sample name Hadza_MoBio_hadza-E-H_I_23_1769__NODE_146_length_127636_cov_10.082111_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745594_bin.118 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;s__UBA636 sp900546285 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_provirus.146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140038 SAMEA13538069 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738261. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538069 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 39.0446 MAG coverage software Reads (ERR7738261) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_I_23_1769__NODE_283_length_91891_cov_23.754014_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585991 sample name Hadza_MoBio_hadza-E-H_I_23_1769__NODE_283_length_91891_cov_23.754014_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738617_provirus.139 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140039 SAMEA13538070 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738261. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538070 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 12.5952 MAG coverage software Reads (ERR7738261) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_MoBio_hadza-E-H_I_23_1769__NODE_716_length_55843_cov_7.778969_1 Viral contig found in MAG ERR7738261_bin.62 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585991 sample name Hadza_MoBio_hadza-E-H_I_23_1769__NODE_716_length_55843_cov_7.778969_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095993 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus;s__Bariatricus comes vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_provirus.716 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140040 SAMEA13538071 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738261. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538071 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 15.99 MAG coverage software Reads (ERR7738261) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_I_23_1769__NODE_1664_length_32340_cov_9.506215 Viral contig found in MAG ERR7738261_bin.12 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585991 sample name Hadza_MoBio_hadza-E-H_I_23_1769__NODE_1664_length_32340_cov_9.506215 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_virus.1973 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140041 SAMEA13538072 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738261. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538072 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 21.7704 MAG coverage software Reads (ERR7738261) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 219 Submitter Id Hadza_MoBio_hadza-E-H_I_23_1769__NODE_285_length_91614_cov_13.181446 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.935483870967742 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585991 sample name Hadza_MoBio_hadza-E-H_I_23_1769__NODE_285_length_91614_cov_13.181446 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_virus.285 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11140042 SAMEA13538073 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738261. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538073 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 37.7629 MAG coverage software Reads (ERR7738261) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560322) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 79 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Hadza_MoBio_hadza-E-H_I_23_1769__NODE_869_length_50253_cov_22.934869 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585991 sample name Hadza_MoBio_hadza-E-H_I_23_1769__NODE_869_length_50253_cov_22.934869 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_virus.773 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140043 SAMEA13538074 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738262. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538074 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 22.3354 MAG coverage software Reads (ERR7738262) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567395) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 420 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_11_THA0065JZ__NODE_456_length_65670_cov_13.106795_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5357142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787398 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_11_THA0065JZ__NODE_456_length_65670_cov_13.106795_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0346573 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140044 SAMEA13538075 2100421 uncultured Caudovirales phage This sample represents an uncultured Minhovirus virus assembled from ERR7738262. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538075 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 5794.56 MAG coverage software Reads (ERR7738262) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567395) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_11_THA0065JZ__NODE_1641_length_19611_cov_3323.641599 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787398 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_11_THA0065JZ__NODE_1641_length_19611_cov_3323.641599 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738262_virus.1641 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Rountreeviridae; Sarlesvirinae; Minhovirus virus enrichment approach none ERS11140045 SAMEA13538076 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738262. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538076 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 449.062 MAG coverage software Reads (ERR7738262) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567395) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 71 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_11_THA0065JZ__NODE_774_length_41762_cov_263.813962 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787398 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_11_THA0065JZ__NODE_774_length_41762_cov_263.813962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_C vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0303461 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140046 SAMEA13538077 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738263. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538077 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 26.7982 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_161_length_146848_cov_16.031948_1 Viral contig found in MAG ERR7738263_bin.40 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7837837837837838 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_161_length_146848_cov_16.031948_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0272478 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140047 SAMEA13538078 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738263. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538078 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 9.94721 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 160 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_299_length_113429_cov_5.789673_1 Viral contig found in MAG ERR7738263_bin.7 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_299_length_113429_cov_5.789673_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.1123 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140048 SAMEA13538079 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738263. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538079 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 76.3404 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 1009 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_52_length_254286_cov_44.562116_1 Viral contig found in MAG ERR7738263_bin.37 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_52_length_254286_cov_44.562116_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.386 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140049 SAMEA13538080 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738263. BACPHLIP temperate score 0.07305889139359004 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538080 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 11.4685 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_913_length_61081_cov_6.524441_1 Viral contig found in MAG ERR7738263_bin.101 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_913_length_61081_cov_6.524441_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME258969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__CAG-269 sp001916005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738263_provirus.913 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140050 SAMEA13538081 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738263. BACPHLIP temperate score 0.2849118942731278 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538081 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:12Z INSDC last update 2022-12-27T00:30:12Z INSDC status public MAG coverage depth 84.695 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_134_length_160185_cov_50.412284 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6607142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_134_length_160185_cov_50.412284 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738167_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFHK01;s__SFHK01 sp004556395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.92 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140051 SAMEA13538082 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738263. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538082 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 17.9457 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_1650_length_39828_cov_10.790144 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_1650_length_39828_cov_10.790144 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.971 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140052 SAMEA13538083 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738263. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538083 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 19.3491 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 112 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_2038_length_33807_cov_11.416513 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_2038_length_33807_cov_11.416513 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746757_virus.1355 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140053 SAMEA13538084 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738263. BACPHLIP temperate score 0.902477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538084 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 7.2982 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_3165_length_23487_cov_4.113071 Viral contig found in MAG ERR7738263_bin.82 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_3165_length_23487_cov_4.113071 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140054 SAMEA13538085 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738263. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538085 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 30.012 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_66_length_222718_cov_18.327473 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.54 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_66_length_222718_cov_18.327473 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738263_virus.66 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140055 SAMEA13538086 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738263. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538086 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 41.2321 MAG coverage software Reads (ERR7738263) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 517 Submitter Id Hadza_MoBio_hadza-I-L_O_17_2510__NODE_986_length_58167_cov_24.774591 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586283 sample name Hadza_MoBio_hadza-I-L_O_17_2510__NODE_986_length_58167_cov_24.774591 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.650 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140056 SAMEA13538087 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738264. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538087 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 8.57335 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 309 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_1947_length_31518_cov_4.827296_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_1947_length_31518_cov_4.827296_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738575_virus.463 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140057 SAMEA13538088 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738264. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538088 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 14.7115 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_407_length_87478_cov_8.673116_1 Viral contig found in MAG ERR7738264_bin.3 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; HMM-based (lower-bound) completeness score 67.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_407_length_87478_cov_8.673116_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-977;g__UBA2903;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_provirus.407 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140058 SAMEA13538089 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738264. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538089 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 24.6987 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_983_length_49974_cov_14.926529_1 Viral contig found in MAG ERR7738264_bin.107 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_983_length_49974_cov_14.926529_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745433_bin.95 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_provirus.983 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140059 SAMEA13538090 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738264. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538090 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 23.6888 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_1196_length_43757_cov_14.141598 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_1196_length_43757_cov_14.141598 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.187853 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140060 SAMEA13538091 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738264. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538091 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 11.9952 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_1634_length_35845_cov_7.080044 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_1634_length_35845_cov_7.080044 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_virus.1634 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140061 SAMEA13538092 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738264. BACPHLIP temperate score 0.0873898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538092 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 11.1065 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 235 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_2083_length_30147_cov_6.585434 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7837837837837838 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_2083_length_30147_cov_6.585434 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738574_virus.239 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140062 SAMEA13538093 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738264. BACPHLIP temperate score 0.1262875439947041 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538093 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 8.63793 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_2899_length_23648_cov_5.032328 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_2899_length_23648_cov_5.032328 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140063 SAMEA13538094 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738264. BACPHLIP temperate score 0.05501014145734777 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538094 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 45.1749 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_3542_length_20285_cov_27.041865 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_3542_length_20285_cov_27.041865 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.3846 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140064 SAMEA13538095 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738264. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538095 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 44.1122 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 168 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_677_length_63660_cov_26.338864 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_677_length_63660_cov_26.338864 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.778 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140065 SAMEA13538096 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738264. BACPHLIP temperate score 0.17129856875493005 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538096 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 22.4725 MAG coverage software Reads (ERR7738264) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_B_13_1594__NODE_916_length_52422_cov_13.477620 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585843 sample name Hadza_MoBio_hadza-A-D_B_13_1594__NODE_916_length_52422_cov_13.477620 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738169_virus.588 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140066 SAMEA13538097 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738265. BACPHLIP temperate score 0.2824339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538097 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 92.3621 MAG coverage software Reads (ERR7738265) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 880 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_23_THA1066YZ__NODE_507_length_54152_cov_55.403329_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787406 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_23_THA1066YZ__NODE_507_length_54152_cov_55.403329_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME239670 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium pseudocatenulatum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738265_provirus.507 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140067 SAMEA13538098 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738265. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538098 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 22.8135 MAG coverage software Reads (ERR7738265) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1854 Number of CRISPR spacer hits supporting host taxonomy 397 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_23_THA1066YZ__NODE_268_length_83275_cov_14.165737 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 11 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.7446808510638298 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787406 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_23_THA1066YZ__NODE_268_length_83275_cov_14.165737 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME283914 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900066565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738653_provirus.102 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140068 SAMEA13538099 2133760 Siphoviridae environmental samples This sample represents an uncultured unclassified Kagunavirus virus assembled from ERR7738265. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538099 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 10.2576 MAG coverage software Reads (ERR7738265) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567500) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_23_THA1066YZ__NODE_649_length_45245_cov_6.110233 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6891891891891891 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787406 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_23_THA1066YZ__NODE_649_length_45245_cov_6.110233 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738265_virus.649 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Guernseyvirinae; Kagunavirus; unclassified Kagunavirus virus enrichment approach none ERS11140069 SAMEA13538100 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738266. BACPHLIP temperate score 0.12951046580442682 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538100 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 30.9583 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_171_length_125421_cov_16.932968_1 Viral contig found in MAG ERR7738266_bin.126 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_171_length_125421_cov_16.932968_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746433_provirus.452 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140070 SAMEA13538101 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738266. BACPHLIP temperate score 0.04234581497797356 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538101 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 23.0735 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_507_length_70536_cov_12.904427_1 Viral contig found in MAG ERR7738266_bin.92 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_507_length_70536_cov_12.904427_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738240_provirus.361 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140071 SAMEA13538102 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738266. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538102 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 33.8881 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_1045_length_44410_cov_19.069361 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_1045_length_44410_cov_19.069361 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.328 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1750;g__UBA7102;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3320 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140072 SAMEA13538103 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738266. BACPHLIP temperate score 0.05247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538103 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 8.23672 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_1304_length_38943_cov_4.540138 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_1304_length_38943_cov_4.540138 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738588_bin.338 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71;s__UBA71 sp006954465 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3667 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140073 SAMEA13538104 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738266. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538104 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 14.3207 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_1660_length_33207_cov_7.963960 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_1660_length_33207_cov_7.963960 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738571_bin.280 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.1529 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140074 SAMEA13538105 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738266. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538105 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 17.4979 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_1963_length_29812_cov_9.860905 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_1963_length_29812_cov_9.860905 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_virus.1483 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140075 SAMEA13538106 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738266. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538106 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 14.8119 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_2614_length_24345_cov_8.248269 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_2614_length_24345_cov_8.248269 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125875 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFFH01;s__SFFH01 sp900542395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745408_virus.411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140076 SAMEA13538107 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738266. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538107 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 15.4491 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_378_length_83708_cov_11.000060 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5652173913043478 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_378_length_83708_cov_11.000060 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140077 SAMEA13538108 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738266. BACPHLIP temperate score 0.1253845907965548 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538108 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 25.6413 MAG coverage software Reads (ERR7738266) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561381) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_A_8_1508__NODE_771_length_54165_cov_14.344624 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585764 sample name Hadza_MoBio_C-REDO_A_8_1508__NODE_771_length_54165_cov_14.344624 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745881_virus.717 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140078 SAMEA13538109 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738267. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538109 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 17.3633 MAG coverage software Reads (ERR7738267) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561865) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_P_18_2352__NODE_1240_length_33215_cov_10.412004_1 Viral contig found in MAG ERR7738267_bin.146 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106182 sample name Hadza_MoBio_hadza-E-H_P_18_2352__NODE_1240_length_33215_cov_10.412004_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.1633 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140079 SAMEA13538110 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7738267. BACPHLIP temperate score 0.05275243220624644 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538110 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 14.9207 MAG coverage software Reads (ERR7738267) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561865) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_P_18_2352__NODE_444_length_62402_cov_9.008263_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106182 sample name Hadza_MoBio_hadza-E-H_P_18_2352__NODE_444_length_62402_cov_9.008263_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_provirus.810 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140080 SAMEA13538111 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738267. BACPHLIP temperate score 0.65 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538111 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 16.7151 MAG coverage software Reads (ERR7738267) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561865) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-E-H_P_18_2352__NODE_91_length_134647_cov_9.611266_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.4918032786885246 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106182 sample name Hadza_MoBio_hadza-E-H_P_18_2352__NODE_91_length_134647_cov_9.611266_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738267_provirus.91 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140081 SAMEA13538112 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738267. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538112 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 337.984 MAG coverage software Reads (ERR7738267) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561865) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_18_2352__NODE_145_length_114131_cov_194.221369 Viral contig found in MAG ERR7738267_bin.99 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9027777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106182 sample name Hadza_MoBio_hadza-E-H_P_18_2352__NODE_145_length_114131_cov_194.221369 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738233_virus.173 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140082 SAMEA13538113 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738267. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538113 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 21.7432 MAG coverage software Reads (ERR7738267) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561865) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_P_18_2352__NODE_2049_length_22701_cov_12.531648 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106182 sample name Hadza_MoBio_hadza-E-H_P_18_2352__NODE_2049_length_22701_cov_12.531648 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.2731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140083 SAMEA13538114 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738267. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538114 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:17Z INSDC last update 2022-12-27T00:30:17Z INSDC status public MAG coverage depth 70.6842 MAG coverage software Reads (ERR7738267) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561865) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 228 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_hadza-E-H_P_18_2352__NODE_451_length_62038_cov_41.345395 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106182 sample name Hadza_MoBio_hadza-E-H_P_18_2352__NODE_451_length_62038_cov_41.345395 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746012_virus.484 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140084 SAMEA13538115 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738268. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538115 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 8.61767 MAG coverage software Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_MoBio_hadza-A-D_E_19_1056__NODE_1565_length_34756_cov_4.889039_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585480 sample name Hadza_MoBio_hadza-A-D_E_19_1056__NODE_1565_length_34756_cov_4.889039_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0276909 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140085 SAMEA13538116 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738268. BACPHLIP temperate score 0.07714757709251101 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538116 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 127.898 MAG coverage software Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 110 Submitter Id Hadza_MoBio_hadza-A-D_E_19_1056__NODE_649_length_63832_cov_77.628013_1 Viral contig found in MAG ERR7738268_bin.194 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585480 sample name Hadza_MoBio_hadza-A-D_E_19_1056__NODE_649_length_63832_cov_77.628013_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_provirus.649 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140086 SAMEA13538117 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738268. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538117 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 24.1115 MAG coverage software Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_E_19_1056__NODE_1347_length_38649_cov_14.257026 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 82.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585480 sample name Hadza_MoBio_hadza-A-D_E_19_1056__NODE_1347_length_38649_cov_14.257026 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745867_virus.243 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140087 SAMEA13538118 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738268. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538118 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 43.7972 MAG coverage software Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_E_19_1056__NODE_1552_length_34982_cov_25.343160 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585480 sample name Hadza_MoBio_hadza-A-D_E_19_1056__NODE_1552_length_34982_cov_25.343160 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.1552 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140088 SAMEA13538119 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738268. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538119 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 23.8812 MAG coverage software Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_E_19_1056__NODE_2079_length_28273_cov_13.710881 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585480 sample name Hadza_MoBio_hadza-A-D_E_19_1056__NODE_2079_length_28273_cov_13.710881 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0379427 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140089 SAMEA13538120 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738268. BACPHLIP temperate score 0.12096128563594025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538120 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 16.0821 MAG coverage software Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_E_19_1056__NODE_2786_length_22211_cov_12.022409 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585480 sample name Hadza_MoBio_hadza-A-D_E_19_1056__NODE_2786_length_22211_cov_12.022409 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.2786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140090 SAMEA13538121 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738268. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538121 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 22.9904 MAG coverage software Reads (ERR7738268) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561917) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 311 Submitter Id Hadza_MoBio_hadza-A-D_E_19_1056__NODE_758_length_58177_cov_13.182754 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6511627906976745 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585480 sample name Hadza_MoBio_hadza-A-D_E_19_1056__NODE_758_length_58177_cov_13.182754 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME283914 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900066565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.758 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140091 SAMEA13538122 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738269. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538122 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 43.5138 MAG coverage software Reads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 341 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_N_14_2337__NODE_171_length_144310_cov_24.490803_1 Viral contig found in MAG ERR7738269_bin.167 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586207 sample name Hadza_MoBio_hadza-E-H_N_14_2337__NODE_171_length_144310_cov_24.490803_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0355909 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140092 SAMEA13538123 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738269. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538123 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 8.82228 MAG coverage software Reads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 192 Submitter Id Hadza_MoBio_hadza-E-H_N_14_2337__NODE_543_length_70292_cov_4.825721_1 Viral contig found in MAG ERR7738269_bin.113 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9655172413793104 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586207 sample name Hadza_MoBio_hadza-E-H_N_14_2337__NODE_543_length_70292_cov_4.825721_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME216999 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales_A;f__UBA1381;g__CAG-41;s__CAG-41 sp900066215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0329916 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140093 SAMEA13538124 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738269. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538124 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 25.6903 MAG coverage software Reads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-E-H_N_14_2337__NODE_1226_length_40260_cov_14.424682 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8484848484848485 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586207 sample name Hadza_MoBio_hadza-E-H_N_14_2337__NODE_1226_length_40260_cov_14.424682 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_virus.1226 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140094 SAMEA13538125 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738269. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538125 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 11.5598 MAG coverage software Reads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_N_14_2337__NODE_1695_length_30746_cov_6.412534 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586207 sample name Hadza_MoBio_hadza-E-H_N_14_2337__NODE_1695_length_30746_cov_6.412534 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745412_virus.1128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140095 SAMEA13538126 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738269. BACPHLIP temperate score 0.20772215993452803 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538126 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 10.7205 MAG coverage software Reads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_N_14_2337__NODE_3608_length_16691_cov_5.998917 Viral contig found in MAG ERR7738269_bin.151 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586207 sample name Hadza_MoBio_hadza-E-H_N_14_2337__NODE_3608_length_16691_cov_5.998917 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745412_virus.3257 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140096 SAMEA13538127 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738269. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538127 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 68.2991 MAG coverage software Reads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 78 Number of CRISPR spacer hits supporting host taxonomy 360 Submitter Id Hadza_MoBio_hadza-E-H_N_14_2337__NODE_783_length_55055_cov_38.330860 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7457627118644068 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586207 sample name Hadza_MoBio_hadza-E-H_N_14_2337__NODE_783_length_55055_cov_38.330860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_virus.783 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140097 SAMEA13538128 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae provirus assembled from ERR7738270. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538128 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 45.0835 MAG coverage software Reads (ERR7738270) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-E-H_E_14_1852__NODE_16_length_284272_cov_27.940858_2 Viral contig found in MAG ERR7738270_bin.52 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586037 sample name Hadza_MoBio_hadza-E-H_E_14_1852__NODE_16_length_284272_cov_27.940858_2 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.1323 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11140098 SAMEA13538129 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738270. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538129 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 29.9872 MAG coverage software Reads (ERR7738270) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_E_14_1852__NODE_593_length_49091_cov_17.953115_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586037 sample name Hadza_MoBio_hadza-E-H_E_14_1852__NODE_593_length_49091_cov_17.953115_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_virus.1159 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140099 SAMEA13538130 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738270. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538130 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 64.8072 MAG coverage software Reads (ERR7738270) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-E-H_E_14_1852__NODE_138_length_102291_cov_37.390622 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9913793103448276 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586037 sample name Hadza_MoBio_hadza-E-H_E_14_1852__NODE_138_length_102291_cov_37.390622 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.255 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11140100 SAMEA13538131 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738270. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538131 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 20.7509 MAG coverage software Reads (ERR7738270) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_14_1852__NODE_258_length_77019_cov_12.629799 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8723404255319149 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586037 sample name Hadza_MoBio_hadza-E-H_E_14_1852__NODE_258_length_77019_cov_12.629799 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_virus.201 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140101 SAMEA13538132 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738270. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538132 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 61.9497 MAG coverage software Reads (ERR7738270) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560494) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_MoBio_hadza-E-H_E_14_1852__NODE_645_length_46848_cov_38.643689 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586037 sample name Hadza_MoBio_hadza-E-H_E_14_1852__NODE_645_length_46848_cov_38.643689 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_virus.471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140102 SAMEA13538133 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738271. BACPHLIP temperate score 0.04730176211453744 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538133 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 8.19703 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_1037_length_48961_cov_4.493065_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_1037_length_48961_cov_4.493065_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140103 SAMEA13538134 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738271. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538134 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 143.957 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 112 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_272_length_102476_cov_84.194133_1 Viral contig found in MAG ERR7738271_bin.46 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_272_length_102476_cov_84.194133_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000434975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.1119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140104 SAMEA13538135 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738271. BACPHLIP temperate score 0.03729583153820043 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538135 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 5.11448 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_10278_length_8422_cov_2.775794 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_10278_length_8422_cov_2.775794 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.9454 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140105 SAMEA13538136 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738271. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538136 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 18.5372 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_1342_length_41777_cov_10.575492 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9117647058823528 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_1342_length_41777_cov_10.575492 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745438_bin.61 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp004553545 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.1197 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140106 SAMEA13538137 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738271. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538137 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 41.5722 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_1660_length_36272_cov_24.146761 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_1660_length_36272_cov_24.146761 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_virus.676 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140107 SAMEA13538138 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738271. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538138 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 31.7088 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_2196_length_29669_cov_18.620539 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_2196_length_29669_cov_18.620539 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_virus.391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140108 SAMEA13538139 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738271. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538139 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 41.5367 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_2674_length_25508_cov_23.942236 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_2674_length_25508_cov_23.942236 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025577 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__SFDB01;s__SFDB01 sp004558825 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746440_virus.1399 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140109 SAMEA13538140 1701671 uncultured podovirus This sample represents an uncultured CrAss-like virus sp. virus assembled from ERR7738271. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538140 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 12.2421 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_333_length_92480_cov_7.041395 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8305084745762712 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_333_length_92480_cov_7.041395 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; CrAss-like virus sp. virus enrichment approach none ERS11140110 SAMEA13538141 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738271. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538141 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 234.846 MAG coverage software Reads (ERR7738271) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_G_3_2391__NODE_722_length_61458_cov_137.354132 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586234 sample name Hadza_MoBio_hadza-I-L_G_3_2391__NODE_722_length_61458_cov_137.354132 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738604_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432655 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745329_virus.181 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140111 SAMEA13538142 2133760 Siphoviridae environmental samples This sample represents an uncultured Lactococcus phage bIL309 provirus assembled from ERR7738272. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538142 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 21.4193 MAG coverage software Reads (ERR7738272) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_167_length_115316_cov_12.335885_2 Viral contig found in MAG ERR7738272_bin.81 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787387 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_167_length_115316_cov_12.335885_2 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME206947 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella;s__Weissella cibaria vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738272_provirus.167_2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lactococcus phage bIL309 virus enrichment approach none ERS11140112 SAMEA13538143 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738272. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538143 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 70.4445 MAG coverage software Reads (ERR7738272) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_429_length_66961_cov_40.133395_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9487179487179488 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787387 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_429_length_66961_cov_40.133395_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140701 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus mucosae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738272_provirus.429 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140113 SAMEA13538144 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738272. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538144 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 286.529 MAG coverage software Reads (ERR7738272) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_1181_length_27123_cov_164.369223 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787387 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_1181_length_27123_cov_164.369223 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738272_virus.1181 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140114 SAMEA13538145 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738272. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538145 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 24.259 MAG coverage software Reads (ERR7738272) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_229_length_98310_cov_14.014466 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787387 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_229_length_98310_cov_14.014466 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098563 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia sp900552665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738535_virus.12 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140115 SAMEA13538146 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738272. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538146 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 110.287 MAG coverage software Reads (ERR7738272) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 118 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_708_length_46024_cov_62.916338 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6041666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787387 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_708_length_46024_cov_62.916338 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0335721 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140116 SAMEA13538147 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738272. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538147 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:18Z INSDC last update 2022-12-27T19:09:18Z INSDC status public MAG coverage depth 20.6519 MAG coverage software Reads (ERR7738272) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_825_length_40004_cov_11.855962 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787387 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_825_length_40004_cov_11.855962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738272_virus.825 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140117 SAMEA13538148 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738272. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538148 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 9.62546 MAG coverage software Reads (ERR7738272) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567287) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_936_length_35540_cov_5.384119 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787387 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_11_RAU1009YZ__NODE_936_length_35540_cov_5.384119 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME103816 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;s__Dorea_A longicatena vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738272_virus.936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140118 SAMEA13538149 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7738273. BACPHLIP temperate score 0.00183820478765556 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538149 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 43.8469 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_141_length_186301_cov_25.324083_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_141_length_186301_cov_25.324083_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_provirus.141 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11140119 SAMEA13538150 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738273. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538150 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 11.9908 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_303_length_132361_cov_10.840275_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_303_length_132361_cov_10.840275_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_provirus.303 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140120 SAMEA13538151 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738273. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538151 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 9.86303 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_747_length_76604_cov_5.636011_1 Viral contig found in MAG ERR7738273_bin.154 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9069767441860463 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_747_length_76604_cov_5.636011_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME121269 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__CAG-115 sp003516865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_provirus.747 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140121 SAMEA13538152 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738273. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538152 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 13.315 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1220_length_55363_cov_7.343143 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1220_length_55363_cov_7.343143 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.708 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140122 SAMEA13538153 1701671 uncultured podovirus This sample represents an uncultured Paenibacillus phage vB_PlaP_API480 virus assembled from ERR7738273. BACPHLIP temperate score 0.01373334967392014 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538153 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 20.6509 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1513_length_47881_cov_11.541691 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1513_length_47881_cov_11.541691 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.1513 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Paenibacillus phage vB_PlaP_API480 virus enrichment approach none ERS11140123 SAMEA13538154 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738273. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538154 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 16.0282 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1670_length_44024_cov_9.053041 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1670_length_44024_cov_9.053041 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME010079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.1020 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140124 SAMEA13538155 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738273. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538155 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 21.2642 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1847_length_40982_cov_11.953893 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1847_length_40982_cov_11.953893 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.1847 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140125 SAMEA13538156 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738273. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538156 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 18.1555 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1985_length_39038_cov_10.134878 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_1985_length_39038_cov_10.134878 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME158618 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__UBA644;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.1985 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140126 SAMEA13538157 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738273. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538157 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 11.0482 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_2217_length_35989_cov_6.151537 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_2217_length_35989_cov_6.151537 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__UBA1234;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.1178 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140127 SAMEA13538158 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7738273. BACPHLIP temperate score 0.11475770925110132 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538158 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 10.8774 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_2547_length_31630_cov_6.294996 Viral contig found in MAG ERR7738273_bin.82 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_2547_length_31630_cov_6.294996 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.1576 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11140128 SAMEA13538159 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738273. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538159 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 11.9006 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_3352_length_24991_cov_7.087220 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_3352_length_24991_cov_7.087220 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.3352 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140129 SAMEA13538160 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738273. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538160 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 58.3746 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_462_length_102153_cov_32.734237 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_462_length_102153_cov_32.734237 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.462 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140130 SAMEA13538161 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738273. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538161 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 9.45332 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_5332_length_16933_cov_5.131882 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 56.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_5332_length_16933_cov_5.131882 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.5332 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140131 SAMEA13538162 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738273. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538162 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 14.5655 MAG coverage software Reads (ERR7738273) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561911) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-A-D_E_17_1054__NODE_857_length_69722_cov_8.173035 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585478 sample name Hadza_MoBio_hadza-A-D_E_17_1054__NODE_857_length_69722_cov_8.173035 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738627_virus.666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140132 SAMEA13538163 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738274. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538163 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 48.3363 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_1238_length_55975_cov_27.485796_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_1238_length_55975_cov_27.485796_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745410_virus.1183 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140133 SAMEA13538164 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738274. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538164 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 17.2384 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 85 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_32_length_320719_cov_9.779446_1 Viral contig found in MAG ERR7738274_bin.229 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9629629629629628 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_32_length_320719_cov_9.779446_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME233621 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D sp000434695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_provirus.88 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140134 SAMEA13538165 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738274. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538165 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 30.008 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 165 Number of CRISPR spacer hits supporting host taxonomy 276 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_786_length_74369_cov_17.015776_1 Viral contig found in MAG ERR7738274_bin.62 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_786_length_74369_cov_17.015776_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_provirus.93 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140135 SAMEA13538166 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738274. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538166 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 24.4642 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 471 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_1280_length_54712_cov_13.999689 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_1280_length_54712_cov_13.999689 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.907 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140136 SAMEA13538167 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738274. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538167 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 8.37278 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_1803_length_43234_cov_4.590426 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_1803_length_43234_cov_4.590426 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745858_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__UMGS1670;s__UMGS1670 sp900553995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1448 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140137 SAMEA13538168 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738274. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538168 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 25.5206 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 191 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_2201_length_37381_cov_15.228635 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7037037037037037 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_2201_length_37381_cov_15.228635 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.2201 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140138 SAMEA13538169 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7738274. BACPHLIP temperate score 0.2753052220829365 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538169 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 9.40013 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_3925_length_23600_cov_5.114399 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_3925_length_23600_cov_5.114399 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738493_provirus.5 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11140139 SAMEA13538170 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738274. BACPHLIP temperate score 0.1193047942582454 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538170 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 23.5597 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_4963_length_19452_cov_13.464694 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_4963_length_19452_cov_13.464694 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737966_virus.2571 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140140 SAMEA13538171 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738274. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538171 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 19.0561 MAG coverage software Reads (ERR7738274) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559904) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 87 Submitter Id Hadza_MoBio_hadza-I-L_K_19_2488__NODE_89_length_212908_cov_10.922041 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 83.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.46296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586262 sample name Hadza_MoBio_hadza-I-L_K_19_2488__NODE_89_length_212908_cov_10.922041 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME099131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000435075 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.89 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140141 SAMEA13538172 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738275. BACPHLIP temperate score 0.525 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538172 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 165.285 MAG coverage software Reads (ERR7738275) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567752) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_187_length_100889_cov_123.109392_1 Viral contig found in MAG ERR7738275_bin.76 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_187_length_100889_cov_123.109392_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.3646 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140142 SAMEA13538173 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738275. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538173 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 50.6205 MAG coverage software Reads (ERR7738275) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567752) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 212 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_53_length_182372_cov_29.549560_1 Viral contig found in MAG ERR7738275_bin.28 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_53_length_182372_cov_29.549560_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737953_virus.234 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140143 SAMEA13538174 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738275. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538174 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 15.4476 MAG coverage software Reads (ERR7738275) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567752) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 354 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_1338_length_37033_cov_9.060288 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_1338_length_37033_cov_9.060288 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738275_virus.1338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140144 SAMEA13538175 336724 Myoviridae environmental samples This sample represents an uncultured Acinetobacter phage MD-2021a virus assembled from ERR7738275. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538175 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 96.9919 MAG coverage software Reads (ERR7738275) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567752) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_1988_length_27921_cov_58.829048 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_1988_length_27921_cov_58.829048 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738275_virus.1988 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Acinetobacter phage MD-2021a virus enrichment approach none ERS11140145 SAMEA13538176 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738275. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538176 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 12.751 MAG coverage software Reads (ERR7738275) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567752) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_3719_length_18042_cov_7.647147 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_3719_length_18042_cov_7.647147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.6060 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140146 SAMEA13538177 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738275. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538177 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 29.3703 MAG coverage software Reads (ERR7738275) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567752) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_616_length_59229_cov_15.317961 Viral contig found in MAG ERR7738275_bin.7 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_616_length_59229_cov_15.317961 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745743_virus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140147 SAMEA13538178 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738275. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27T19:09:17Z ENA-LAST-UPDATE 2022-12-27T19:09:17Z External Id SAMEA13538178 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 118.751 MAG coverage software Reads (ERR7738275) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567752) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1280 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_884_length_48567_cov_73.579666 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586149 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_2_2185__NODE_884_length_48567_cov_73.579666 scientific_name Siphoviridae environmental samples sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738275_virus.884 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae ERS11140148 SAMEA13538179 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738276. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538179 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 11.6692 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_1466_length_46023_cov_7.038850_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_1466_length_46023_cov_7.038850_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_provirus.1466 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140149 SAMEA13538180 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738276. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538180 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 22.2363 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_24_length_345304_cov_13.536299_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7096774193548387 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_24_length_345304_cov_13.536299_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q;s__Clostridium_Q sp003024715 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_provirus.24 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140150 SAMEA13538181 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738276. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538181 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 12.1929 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_48_length_285625_cov_7.249328_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5645161290322581 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_48_length_285625_cov_7.249328_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373831 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140151 SAMEA13538182 336724 Myoviridae environmental samples This sample represents an uncultured Hpunavirus provirus assembled from ERR7738276. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538182 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 42.905 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_909_length_66394_cov_25.570563_1 Viral contig found in MAG ERR7738276_bin.152 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7352941176470589 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_909_length_66394_cov_25.570563_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME266127 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter;s__Aggregatibacter segnis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_provirus.909 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Peduovirinae; Hpunavirus virus enrichment approach none ERS11140152 SAMEA13538183 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738276. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538183 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 13.6378 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 90 Number of CRISPR spacer hits supporting host taxonomy 1137 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_1403_length_47688_cov_8.115457 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6944444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_1403_length_47688_cov_8.115457 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140153 SAMEA13538184 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738276. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538184 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 13.5187 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_1589_length_42982_cov_8.022795 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_1589_length_42982_cov_8.022795 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_virus.1589 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140154 SAMEA13538185 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738276. BACPHLIP temperate score 0.04966960352422907 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538185 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 23.8791 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 190 Number of CRISPR spacer hits supporting host taxonomy 732 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_1824_length_37996_cov_14.474010 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_1824_length_37996_cov_14.474010 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.561 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140155 SAMEA13538186 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738276. BACPHLIP temperate score 0.714977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538186 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 10.801 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 462 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_2425_length_29786_cov_6.288195 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_2425_length_29786_cov_6.288195 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_virus.2425 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140156 SAMEA13538187 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738276. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538187 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 59.9956 MAG coverage software Reads (ERR7738276) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558871) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Pilot_MoBio_Fiber_C_5_1018__NODE_343_length_115602_cov_36.134153 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5405405405405406 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383844 sample name Pilot_MoBio_Fiber_C_5_1018__NODE_343_length_115602_cov_36.134153 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_virus.343 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140157 SAMEA13538188 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738277. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538188 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 10.4507 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_145_length_104708_cov_5.794287_1 Viral contig found in MAG ERR7738277_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_145_length_104708_cov_5.794287_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_provirus.145 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140158 SAMEA13538189 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus provirus assembled from ERR7738277. BACPHLIP temperate score 0.05195538818076477 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538189 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 229.261 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 90 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_37_length_204844_cov_129.782607_1 Viral contig found in MAG ERR7738277_bin.54 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_37_length_204844_cov_129.782607_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_provirus.37 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11140159 SAMEA13538190 1701671 uncultured podovirus This sample represents an uncultured Aeromonas phage phiARM81mr virus assembled from ERR7738277. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538190 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 437.719 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_1111_length_31939_cov_264.447806 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_1111_length_31939_cov_264.447806 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.1111 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Aeromonas phage phiARM81mr virus enrichment approach none ERS11140160 SAMEA13538191 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738277. BACPHLIP temperate score 0.14936728245389252 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538191 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 7.9292 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 243 Number of CRISPR spacer hits supporting host taxonomy 146 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_1719_length_22595_cov_4.164357 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_1719_length_22595_cov_4.164357 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0226686 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140161 SAMEA13538192 2133760 Siphoviridae environmental samples This sample represents an uncultured Maenadvirus virus assembled from ERR7738277. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538192 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 376.259 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_252_length_79561_cov_210.698795 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8018867924528302 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_252_length_79561_cov_210.698795 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738260_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus;s__Lactiplantibacillus plantarum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.252 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Tybeckvirinae; Maenadvirus virus enrichment approach none ERS11140162 SAMEA13538193 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738277. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538193 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 39.4374 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_508_length_52122_cov_22.189355 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_508_length_52122_cov_22.189355 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140163 SAMEA13538194 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738277. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538194 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 365.153 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_657_length_45107_cov_205.585165 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_657_length_45107_cov_205.585165 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738551_virus.440 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140164 SAMEA13538195 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738277. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538195 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 86.1137 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_780_length_40759_cov_49.122782 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_780_length_40759_cov_49.122782 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746779_virus.1100 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140165 SAMEA13538196 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738277. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538196 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 42.0084 MAG coverage software Reads (ERR7738277) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567191) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_910_length_36631_cov_26.219976 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787347 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_910_length_36631_cov_26.219976 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.910 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140166 SAMEA13538197 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738278. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538197 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 20.8833 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1122_length_50039_cov_13.054121_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1122_length_50039_cov_13.054121_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_provirus.1122 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140167 SAMEA13538198 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738278. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538198 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 21.0528 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_207_length_129718_cov_12.838060_1 Viral contig found in MAG ERR7738278_bin.76 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.951219512195122 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_207_length_129718_cov_12.838060_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.269 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS363;s__UMGS363 sp900543105 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_provirus.207 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140168 SAMEA13538199 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738278. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538199 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 34.5476 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_952_length_55912_cov_21.748384_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_952_length_55912_cov_21.748384_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_provirus.808 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140169 SAMEA13538200 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738278. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538200 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 14.855 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 173 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1286_length_45149_cov_9.046836 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1286_length_45149_cov_9.046836 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745755_provirus.795 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140170 SAMEA13538201 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738278. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538201 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 37.4038 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1435_length_41547_cov_22.607982 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7837837837837838 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1435_length_41547_cov_22.607982 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.1435 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140171 SAMEA13538202 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738278. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538202 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 56.5592 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1659_length_36923_cov_34.064186 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6129032258064516 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1659_length_36923_cov_34.064186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME176098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.1659 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140172 SAMEA13538203 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738278. BACPHLIP temperate score 0.3004947229551451 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538203 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 71.6475 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 242 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1989_length_31737_cov_43.833607 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_1989_length_31737_cov_43.833607 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.1989 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140173 SAMEA13538204 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738278. BACPHLIP temperate score 0.00247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538204 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 12.7811 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_3123_length_21790_cov_7.740616 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_3123_length_21790_cov_7.740616 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746285_bin.189 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_virus.5176 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140174 SAMEA13538205 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738278. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538205 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 19.277 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_3888_length_18248_cov_11.715646 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; HMM-based (lower-bound) completeness score 61.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_3888_length_18248_cov_11.715646 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.3888 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140175 SAMEA13538206 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738278. BACPHLIP temperate score 0.08312057094440387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538206 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 38.1321 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_6231_length_12335_cov_23.394940 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_6231_length_12335_cov_23.394940 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.105 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp900552845 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.6231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140176 SAMEA13538207 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738278. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538207 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 215.432 MAG coverage software Reads (ERR7738278) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562243) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 235 Submitter Id Hadza_MoBio_hadza-I-L_L_3_1264__NODE_864_length_59043_cov_129.578418 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9210526315789472 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585682 sample name Hadza_MoBio_hadza-I-L_L_3_1264__NODE_864_length_59043_cov_129.578418 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_provirus.591 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140177 SAMEA13538208 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738352. BACPHLIP temperate score 0.12637530562347188 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538208 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 17.3496 MAG coverage software Reads (ERR7738352) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_279_length_80314_cov_9.787392_1 Viral contig found in MAG ERR7738352_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787386 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_279_length_80314_cov_9.787392_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738352_provirus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140178 SAMEA13538209 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738352. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538209 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 8.67896 MAG coverage software Reads (ERR7738352) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1378 Number of CRISPR spacer hits supporting host taxonomy 187 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_816_length_38466_cov_4.808096_1 Viral contig found in MAG ERR7738352_bin.15 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787386 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_816_length_38466_cov_4.808096_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola dorei vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738564_provirus.163 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140179 SAMEA13538210 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738352. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538210 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 11.8252 MAG coverage software Reads (ERR7738352) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 251 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_433_length_62305_cov_6.677059 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8085106382978723 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787386 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_433_length_62305_cov_6.677059 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147876 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides merdae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738352_virus.433 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11140180 SAMEA13538211 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738352. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538211 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 7.80048 MAG coverage software Reads (ERR7738352) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1213 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_685_length_44086_cov_4.248290 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787386 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_685_length_44086_cov_4.248290 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0352447 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140181 SAMEA13538212 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738352. BACPHLIP temperate score 0.05214757709251101 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538212 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 13.13 MAG coverage software Reads (ERR7738352) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 166 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_901_length_35971_cov_7.340698 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787386 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_9_RAU0028AZ__NODE_901_length_35971_cov_7.340698 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098563 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia sp900552665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738352_virus.901 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140182 SAMEA13538213 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738353. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538213 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 223.299 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_236_length_103411_cov_123.186647_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_236_length_103411_cov_123.186647_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745836_virus.193 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140183 SAMEA13538214 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738353. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538214 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 118.951 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_419_length_76536_cov_68.419310_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_419_length_76536_cov_68.419310_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.1999 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140184 SAMEA13538215 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738353. BACPHLIP temperate score 0.16857916465189376 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538215 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 17.6921 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_99_length_149282_cov_9.911732_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_99_length_149282_cov_9.911732_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_provirus.411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140185 SAMEA13538216 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738353. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538216 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 9.57827 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_1179_length_39874_cov_5.200266 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_1179_length_39874_cov_5.200266 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.1179 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140186 SAMEA13538217 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738353. BACPHLIP temperate score 0.525 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538217 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 15.3631 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_132_length_135825_cov_8.687119 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 78.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_132_length_135825_cov_8.687119 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.132 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140187 SAMEA13538218 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738353. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538218 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 97.4814 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 439 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_1547_length_33095_cov_54.213066 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_1547_length_33095_cov_54.213066 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001027 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus sp900066115 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.1547 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140188 SAMEA13538219 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738353. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538219 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 27.3999 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_1912_length_28509_cov_15.331422 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_1912_length_28509_cov_15.331422 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140189 SAMEA13538220 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738353. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538220 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 29.849 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_2379_length_24200_cov_16.838246 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_2379_length_24200_cov_16.838246 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.2379 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140190 SAMEA13538221 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738353. BACPHLIP temperate score 0.0322136563876652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538221 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 288.676 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_3223_length_19090_cov_161.691053 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_3223_length_19090_cov_161.691053 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_provirus.2016 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140191 SAMEA13538222 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7738353. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538222 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 33.5476 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_51_length_190658_cov_18.777968 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.5128205128205128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_51_length_190658_cov_18.777968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.63 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11140192 SAMEA13538223 2133760 Siphoviridae environmental samples This sample represents an uncultured Enterobacteria phage mEp021 virus assembled from ERR7738353. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538223 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 12.1561 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_691_length_55804_cov_6.672493 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8313253012048193 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_691_length_55804_cov_6.672493 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.691 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Enterobacteria phage mEp021 virus enrichment approach none ERS11140193 SAMEA13538224 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738353. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538224 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 15.9527 MAG coverage software Reads (ERR7738353) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567219) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 279 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_896_length_47946_cov_9.032923 Viral contig found in MAG ERR7738353_bin.165 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6060606060606061 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787344 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_15_CHE1003TZ__NODE_896_length_47946_cov_9.032923 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.896 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140194 SAMEA13538225 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738426. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538225 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 76.8417 MAG coverage software Reads (ERR7738426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567233) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 147 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_205_length_103756_cov_44.951851_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787379 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_205_length_103756_cov_44.951851_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738426_provirus.205 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140195 SAMEA13538226 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738426. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538226 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 16.8454 MAG coverage software Reads (ERR7738426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567233) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 270 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_610_length_55229_cov_9.832427_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787379 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_610_length_55229_cov_9.832427_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147876 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides merdae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738426_provirus.610 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140196 SAMEA13538227 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738426. BACPHLIP temperate score 0.17747797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538227 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 16.7231 MAG coverage software Reads (ERR7738426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567233) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 70 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_1070_length_35620_cov_9.855555 Viral contig found in MAG ERR7738426_bin.13 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787379 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_1070_length_35620_cov_9.855555 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096004 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__Desulfovibrio piger vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738426_virus.1070 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140197 SAMEA13538228 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738426. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538228 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 27.0426 MAG coverage software Reads (ERR7738426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567233) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_254_length_93872_cov_15.641836 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787379 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_254_length_93872_cov_15.641836 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001734 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides uniformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738426_virus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140198 SAMEA13538229 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738426. BACPHLIP temperate score 0.0255538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538229 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 22.6325 MAG coverage software Reads (ERR7738426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567233) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 107 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_728_length_48719_cov_13.266642 Viral contig found in MAG ERR7738426_bin.73 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787379 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_21_RAJ1012YZ__NODE_728_length_48719_cov_13.266642 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096004 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__Desulfovibrio piger vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738426_virus.728 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140199 SAMEA13538230 2133760 Siphoviridae environmental samples This sample represents an uncultured Streptococcus phage Javan351 provirus assembled from ERR7738433. BACPHLIP temperate score 0.02973568281938326 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538230 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 8.83723 MAG coverage software Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_1714_length_24645_cov_5.023893_1 Viral contig found in MAG ERR7738433_bin.138 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787342 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_1714_length_24645_cov_5.023893_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745859_provirus.2938 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Streptococcus phage Javan351 virus enrichment approach none ERS11140200 SAMEA13538231 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738433. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538231 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 11.297 MAG coverage software Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_642_length_49065_cov_6.520046_1 Viral contig found in MAG ERR7738433_bin.57 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787342 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_642_length_49065_cov_6.520046_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738433_provirus.642 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140201 SAMEA13538232 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738433. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538232 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 221.241 MAG coverage software Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 685 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_1184_length_33233_cov_128.725600 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787342 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_1184_length_33233_cov_128.725600 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001027 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus sp900066115 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738433_virus.1184 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140202 SAMEA13538233 1701671 uncultured podovirus This sample represents an uncultured CrAss-like virus sp. virus assembled from ERR7738433. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538233 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 11.3815 MAG coverage software Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_223_length_98796_cov_6.503763 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 25 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.5154639175257731 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787342 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_223_length_98796_cov_6.503763 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738240_virus.289 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; CrAss-like virus sp. virus enrichment approach none ERS11140203 SAMEA13538234 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738433. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538234 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:29Z INSDC last update 2022-12-27T00:30:29Z INSDC status public MAG coverage depth 31.9951 MAG coverage software Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_404_length_66322_cov_18.678466 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787342 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_404_length_66322_cov_18.678466 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000247 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter;s__Intestinibacter bartlettii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.340 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140204 SAMEA13538235 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738433. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538235 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 6.9769 MAG coverage software Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_7967_length_7206_cov_3.956095 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787342 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_7967_length_7206_cov_3.956095 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738433_virus.7967 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140205 SAMEA13538236 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738433. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538236 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 22.5564 MAG coverage software Reads (ERR7738433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567237) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 218 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_978_length_38007_cov_13.115028 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5757575757575758 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787342 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_11_CHE0013BZ__NODE_978_length_38007_cov_13.115028 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738433_virus.978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140206 SAMEA13538237 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738447. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538237 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 191.645 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 369 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1309_length_50395_cov_126.431357_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1309_length_50395_cov_126.431357_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.2604 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140207 SAMEA13538238 1478972 Gokushovirinae environmental samples This sample represents an uncultured Gokushovirus WZ-2015a provirus assembled from ERR7738447. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538238 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 289.292 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_3592_length_22717_cov_171.620716_1 Viral contig found in MAG ERR7738447_bin.292 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_3592_length_22717_cov_171.620716_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_provirus.3592 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; unclassified Gokushovirinae; Gokushovirus WZ-2015a virus enrichment approach none ERS11140208 SAMEA13538239 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738447. BACPHLIP temperate score 0.1426160506300154 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538239 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 15.7234 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 112 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_636_length_80148_cov_9.086636_1 Viral contig found in MAG ERR7738447_bin.175 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_636_length_80148_cov_9.086636_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738616_bin.92 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_provirus.636 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140209 SAMEA13538240 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738447. BACPHLIP temperate score 0.3875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538240 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 36.9976 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_107_length_179566_cov_21.896551 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.984126984126984 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_107_length_179566_cov_21.896551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.132 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140210 SAMEA13538241 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738447. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538241 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 22.8479 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1425_length_47822_cov_13.184606 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5357142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1425_length_47822_cov_13.184606 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.386 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140211 SAMEA13538242 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738447. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538242 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 950.228 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1608_length_43612_cov_529.220489 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1608_length_43612_cov_529.220489 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745823_bin.49 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001;s__SFJ001 sp004555865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_virus.928 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140212 SAMEA13538243 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738447. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538243 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 46.8881 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1968_length_37805_cov_27.161631 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_1968_length_37805_cov_27.161631 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.1968 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140213 SAMEA13538244 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738447. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538244 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 10.0019 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_2244_length_34006_cov_5.515400 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_2244_length_34006_cov_5.515400 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140214 SAMEA13538245 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738447. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538245 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 46.1526 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_2405_length_31913_cov_26.008292 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_2405_length_31913_cov_26.008292 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257123 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900547315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_provirus.308 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140215 SAMEA13538246 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738447. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538246 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 8.0306 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_2902_length_27239_cov_4.102496 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_2902_length_27239_cov_4.102496 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.2902 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140216 SAMEA13538247 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738447. BACPHLIP temperate score 0.1673458149779736 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538247 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 7.1745 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_3740_length_22035_cov_3.626696 Viral contig found in MAG ERR7738447_bin.173 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_3740_length_22035_cov_3.626696 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746094_bin.4 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.3740 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140217 SAMEA13538248 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738447. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538248 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 37.0507 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_4713_length_18143_cov_21.441769 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_4713_length_18143_cov_21.441769 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.4713 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140218 SAMEA13538249 336724 Myoviridae environmental samples This sample represents an uncultured Phage DP SC_6_H4_2017 virus assembled from ERR7738447. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538249 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 131.747 MAG coverage software Reads (ERR7738447) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561837) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_A_22_1120__NODE_648_length_79039_cov_75.559193 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585544 sample name Hadza_MoBio_hadza-A-D_A_22_1120__NODE_648_length_79039_cov_75.559193 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.429 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Phage DP SC_6_H4_2017 virus enrichment approach none ERS11140219 SAMEA13538250 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738451. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538250 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 1218.58 MAG coverage software Reads (ERR7738451) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567433) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 71 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_118_length_131066_cov_749.239318_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.38235294117647056 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787399 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_118_length_131066_cov_749.239318_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738645_virus.327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140220 SAMEA13538251 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738451. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538251 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 11.4542 MAG coverage software Reads (ERR7738451) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567433) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_543_length_55040_cov_6.497207_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787399 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_543_length_55040_cov_6.497207_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738451_provirus.543 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140221 SAMEA13538252 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738451. BACPHLIP temperate score 0.07897769092469892 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538252 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 7.69115 MAG coverage software Reads (ERR7738451) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567433) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_1643_length_22653_cov_4.122962 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787399 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_1643_length_22653_cov_4.122962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0302247 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140222 SAMEA13538253 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738451. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538253 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 157.782 MAG coverage software Reads (ERR7738451) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567433) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 81 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_433_length_62624_cov_88.704734 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787399 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_433_length_62624_cov_88.704734 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0370616 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140223 SAMEA13538254 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738451. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538254 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 21.0106 MAG coverage software Reads (ERR7738451) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567433) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_90_length_151784_cov_11.820252 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 17 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.5423728813559322 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787399 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_23_THA0068JZ__NODE_90_length_151784_cov_11.820252 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738530_bin.33 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium sp900539945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738451_virus.90 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140224 SAMEA13538255 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738460. BACPHLIP temperate score 0.0293080874004698 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538255 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 8.07865 MAG coverage software Reads (ERR7738460) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567617) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ__NODE_1630_length_44043_cov_4.444298_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106185 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ__NODE_1630_length_44043_cov_4.444298_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738460_provirus.1630 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140225 SAMEA13538256 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7738460. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538256 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 10.8318 MAG coverage software Reads (ERR7738460) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567617) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ__NODE_1484_length_46840_cov_6.180142 Viral contig found in MAG ERR7738460_bin.178 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106185 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ__NODE_1484_length_46840_cov_6.180142 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738460_virus.1484 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11140226 SAMEA13538257 2133760 Siphoviridae environmental samples This sample represents an uncultured unclassified Decurrovirus virus assembled from ERR7738460. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538257 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 75.5024 MAG coverage software Reads (ERR7738460) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567617) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ__NODE_5433_length_17545_cov_43.745134 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106185 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ__NODE_5433_length_17545_cov_43.745134 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738460_virus.5433 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Decurrovirus; unclassified Decurrovirus virus enrichment approach none ERS11140227 SAMEA13538258 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage provirus assembled from ERR7738461. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538258 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 20.8185 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_129_length_136576_cov_12.571286_1 Viral contig found in MAG ERR7738461_bin.107 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_129_length_136576_cov_12.571286_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270564 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738141_virus.327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11140228 SAMEA13538259 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738461. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538259 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:35Z INSDC last update 2022-12-27T00:30:35Z INSDC status public MAG coverage depth 15.841 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 62 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_412_length_86458_cov_9.542017_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 42.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_412_length_86458_cov_9.542017_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.267 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140229 SAMEA13538260 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. provirus assembled from ERR7738461. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538260 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 11.7159 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_8137_length_11169_cov_6.960512_1 Viral contig found in MAG ERR7738461_bin.124 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_8137_length_11169_cov_6.960512_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_provirus.8137 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140230 SAMEA13538261 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738461. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538261 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 12.1093 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 155 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_1215_length_45047_cov_7.248677 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5128205128205128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_1215_length_45047_cov_7.248677 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.1517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140231 SAMEA13538262 1701671 uncultured podovirus This sample represents an uncultured Roseobacter phage CRP-7 virus assembled from ERR7738461. BACPHLIP temperate score 0.6873898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538262 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 169.947 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_1686_length_36751_cov_101.730190 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_1686_length_36751_cov_101.730190 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.72 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Roseobacter phage CRP-7 virus enrichment approach none ERS11140232 SAMEA13538263 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738461. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538263 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 41.0179 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_1970_length_33167_cov_22.796525 Viral contig found in MAG ERR7738461_bin.7 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_1970_length_33167_cov_22.796525 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196;s__CAG-196 sp900553895 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.3054 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140233 SAMEA13538264 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738461. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538264 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 41.6913 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 104 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_2362_length_29277_cov_25.482774 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_2362_length_29277_cov_25.482774 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1989 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140234 SAMEA13538265 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7738461. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538265 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 22.1312 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_2809_length_25881_cov_12.499612 Viral contig found in MAG ERR7738461_bin.7 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_2809_length_25881_cov_12.499612 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745918_bin.153 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.32 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11140235 SAMEA13538266 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738461. BACPHLIP temperate score 0.06497797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538266 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 10.6938 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_4179_length_18979_cov_6.465348 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_4179_length_18979_cov_6.465348 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.1580 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140236 SAMEA13538267 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738461. BACPHLIP temperate score 0.6125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538267 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 855.701 MAG coverage software Reads (ERR7738461) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567674) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 316 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_815_length_57720_cov_513.699166 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586225 sample name Hadza_PheChl_Fiber-Hadza-Nepal_K_2_2358__NODE_815_length_57720_cov_513.699166 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738267_virus.372 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140237 SAMEA13538268 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738472. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538268 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 28.0492 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1385_length_46326_cov_16.379165_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9130434782608696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1385_length_46326_cov_16.379165_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_provirus.1385 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140238 SAMEA13538269 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738472. BACPHLIP temperate score 0.20049472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538269 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 24.6671 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 770 Number of CRISPR spacer hits supporting host taxonomy 223 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_506_length_94749_cov_14.496683_1 Viral contig found in MAG ERR7738472_bin.157 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_506_length_94749_cov_14.496683_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0258741 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140239 SAMEA13538270 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738472. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538270 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 24.1471 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_980_length_60848_cov_14.288049_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.902439024390244 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_980_length_60848_cov_14.288049_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_provirus.980 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140240 SAMEA13538271 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738472. BACPHLIP temperate score 0.14558091782530816 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538271 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 88.2766 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 293 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1156_length_53469_cov_54.233462 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 75.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1156_length_53469_cov_54.233462 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.1156 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11140241 SAMEA13538272 2133760 Siphoviridae environmental samples This sample represents an uncultured Psavirus virus assembled from ERR7738472. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538272 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 53.9619 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1370_length_46794_cov_31.246441 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1370_length_46794_cov_31.246441 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.1370 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Psavirus virus enrichment approach none ERS11140242 SAMEA13538273 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738472. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538273 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 9.8196 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1502_length_42877_cov_5.674790 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8378378378378378 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1502_length_42877_cov_5.674790 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.328 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1750;g__UBA7102;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.1502 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140243 SAMEA13538274 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738472. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538274 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 448.267 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1663_length_39624_cov_259.747794 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.43478260869565216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1663_length_39624_cov_259.747794 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.1663 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140244 SAMEA13538275 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738472. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538275 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 23.1878 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 340 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1808_length_36820_cov_13.323844 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_1808_length_36820_cov_13.323844 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.1808 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140245 SAMEA13538276 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738472. BACPHLIP temperate score 0.08869765791341377 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538276 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 35.7231 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 400 Number of CRISPR spacer hits supporting host taxonomy 506 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_2108_length_32522_cov_20.910402 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4827586206896552 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_2108_length_32522_cov_20.910402 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140246 SAMEA13538277 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738472. BACPHLIP temperate score 0.00247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538277 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 29.8981 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 125 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_2432_length_28340_cov_17.529455 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_2432_length_28340_cov_17.529455 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.2432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140247 SAMEA13538278 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Ceridwen virus assembled from ERR7738472. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538278 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 24.1785 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_2864_length_24503_cov_14.387251 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_2864_length_24503_cov_14.387251 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.2864 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Butyrivibrio virus Ceridwen virus enrichment approach none ERS11140248 SAMEA13538279 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738472. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538279 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 9.14918 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_3946_length_18055_cov_5.163867 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_3946_length_18055_cov_5.163867 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.3946 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140249 SAMEA13538280 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738472. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538280 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 2955.88 MAG coverage software Reads (ERR7738472) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_975_length_60974_cov_1703.058739 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787389 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_15_RAU1013YZ__NODE_975_length_60974_cov_1703.058739 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.975 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140250 SAMEA13538281 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738493. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538281 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 12.3655 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_256_length_151653_cov_7.451503_1 Viral contig found in MAG ERR7738493_bin.209 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_256_length_151653_cov_7.451503_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA1829;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738493_provirus.256 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140251 SAMEA13538282 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738493. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538282 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 205.632 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 316 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_675_length_85641_cov_125.196333_1 Viral contig found in MAG ERR7738493_bin.110 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_675_length_85641_cov_125.196333_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME232472 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-288;g__CAG-568;s__CAG-568 sp000434395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738493_provirus.675 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140252 SAMEA13538283 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738493. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538283 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 110.002 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_135_length_204886_cov_66.586766 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 12 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_135_length_204886_cov_66.586766 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738493_virus.135 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140253 SAMEA13538284 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738493. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538284 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 41.9 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_1574_length_43481_cov_25.633144 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_1574_length_43481_cov_25.633144 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124703 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_virus.1371 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140254 SAMEA13538285 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738493. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538285 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 33.4361 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 116 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_1763_length_39034_cov_19.909131 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_1763_length_39034_cov_19.909131 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140255 SAMEA13538286 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738493. BACPHLIP temperate score 0.3799559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538286 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 58.2952 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_1980_length_35123_cov_35.591936 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_1980_length_35123_cov_35.591936 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_provirus.8 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140256 SAMEA13538287 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738493. BACPHLIP temperate score 0.05991189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538287 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 8.98897 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_2579_length_27176_cov_5.228459 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_2579_length_27176_cov_5.228459 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0281755 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140257 SAMEA13538288 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738493. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538288 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 297.032 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 161 Number of CRISPR spacer hits supporting host taxonomy 295 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_4085_length_17039_cov_178.744311 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_4085_length_17039_cov_178.744311 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140258 SAMEA13538289 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738493. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538289 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 53.142 MAG coverage software Reads (ERR7738493) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567297) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_532_length_101473_cov_32.843367 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787384 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_15_RAU0016YZ__NODE_532_length_101473_cov_32.843367 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738551_bin.104 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia sp900756925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738493_virus.532 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140259 SAMEA13538290 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738513. BACPHLIP temperate score 0.04054736765072696 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538290 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 62.0238 MAG coverage software Reads (ERR7738513) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567487) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 193 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_1064_length_39477_cov_35.087335_1 Viral contig found in MAG ERR7738513_bin.6 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787408 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_1064_length_39477_cov_35.087335_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME246739 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;s__Lachnospira eligens_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738513_provirus.1064 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140260 SAMEA13538291 2133760 Siphoviridae environmental samples This sample represents an uncultured Streptococcus phage Javan351 provirus assembled from ERR7738513. BACPHLIP temperate score 0.04655891240983966 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538291 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:36Z INSDC last update 2022-12-27T00:30:36Z INSDC status public MAG coverage depth 29.9881 MAG coverage software Reads (ERR7738513) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567487) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_353_length_96217_cov_17.145070_1 Viral contig found in MAG ERR7738513_bin.110 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787408 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_353_length_96217_cov_17.145070_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375;s__UMGS1375 sp900066615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738513_provirus.353 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Streptococcus phage Javan351 virus enrichment approach none ERS11140261 SAMEA13538292 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738513. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538292 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 26.8075 MAG coverage software Reads (ERR7738513) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567487) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_669_length_60162_cov_15.170192_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.926829268292683 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787408 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_669_length_60162_cov_15.170192_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_provirus.980 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140262 SAMEA13538293 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7738513. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538293 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 12.7404 MAG coverage software Reads (ERR7738513) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567487) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_1199_length_35204_cov_7.083241 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.45714285714285713 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787408 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_1199_length_35204_cov_7.083241 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738513_virus.1199 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11140263 SAMEA13538294 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738513. BACPHLIP temperate score 0.6125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538294 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 8.36324 MAG coverage software Reads (ERR7738513) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567487) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 152 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_2034_length_20913_cov_4.350451 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787408 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_2034_length_20913_cov_4.350451 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME232880 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A;s__Fusobacterium_A mortiferum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738513_virus.2034 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140264 SAMEA13538295 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738513. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538295 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 11.2344 MAG coverage software Reads (ERR7738513) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567487) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_858_length_48477_cov_6.222500 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787408 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_13_THA1070JZ__NODE_858_length_48477_cov_6.222500 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738513_virus.858 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140265 SAMEA13538296 2100421 uncultured Caudovirales phage This sample represents an uncultured Akkermansia phage DTMo-2021a provirus assembled from ERR7738514. BACPHLIP temperate score 0.11299472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538296 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 89.7722 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 67 Number of CRISPR spacer hits supporting host taxonomy 707 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_1522_length_55695_cov_50.905498_1 Viral contig found in MAG ERR7738514_bin.33 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_1522_length_55695_cov_50.905498_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738514_provirus.1522 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Akkermansia phage DTMo-2021a virus enrichment approach none ERS11140266 SAMEA13538297 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738514. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538297 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 45.9323 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 105 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_3151_length_29375_cov_27.382245_1 Viral contig found in MAG ERR7738514_bin.92 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_3151_length_29375_cov_27.382245_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME121515 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20;s__51-20 sp001917175 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0244827 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140267 SAMEA13538298 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe provirus assembled from ERR7738514. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538298 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 56.196 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 531 Number of CRISPR spacer hits supporting host taxonomy 1343 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_585_length_108532_cov_32.698852_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_585_length_108532_cov_32.698852_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11140268 SAMEA13538299 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738514. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538299 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 9.83146 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 343 Number of CRISPR spacer hits supporting host taxonomy 241 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_932_length_78469_cov_5.478965_1 Viral contig found in MAG ERR7738514_bin.171 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7560975609756098 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_932_length_78469_cov_5.478965_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738514_provirus.932 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140269 SAMEA13538300 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738514. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538300 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 982.335 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 131 Number of CRISPR spacer hits supporting host taxonomy 396 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_1555_length_54700_cov_552.940135 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_1555_length_54700_cov_552.940135 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0370200 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140270 SAMEA13538301 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738514. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538301 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 39.014 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_1960_length_45366_cov_22.213518 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.43478260869565216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_1960_length_45366_cov_22.213518 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0330522 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140271 SAMEA13538302 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738514. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538302 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:45Z INSDC last update 2022-12-27T00:30:45Z INSDC status public MAG coverage depth 20.7088 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 138 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_2184_length_41490_cov_11.844131 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_2184_length_41490_cov_11.844131 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738547_virus.1799 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140272 SAMEA13538303 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738514. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538303 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 11.0794 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 172 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_2898_length_31785_cov_6.252618 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_2898_length_31785_cov_6.252618 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0338577 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140273 SAMEA13538304 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738514. BACPHLIP temperate score 0.1748898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538304 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 60.2081 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_356_length_144896_cov_34.042916 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 29 number of unique standard tRNAs extracted 20 percent of BLAST hits supporting viral taxonomy 0.7037037037037037 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_356_length_144896_cov_34.042916 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0375643 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140274 SAMEA13538305 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738514. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538305 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 65.8048 MAG coverage software Reads (ERR7738514) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567069) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_72_length_293869_cov_37.211306 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; HMM-based (lower-bound) completeness score 94.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 23 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383944 sample name Pilot_MoBio_Fiber-Hadza-Nepal_C_23_7024__NODE_72_length_293869_cov_37.211306 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.15 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140275 SAMEA13538306 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738515. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538306 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 38.0287 MAG coverage software Reads (ERR7738515) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567081) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 69 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_2_length_686296_cov_22.377683_1 Viral contig found in MAG ERR7738515_bin.2 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8214285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787338 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_2_length_686296_cov_22.377683_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738515_provirus.2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140276 SAMEA13538307 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738515. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538307 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 50.0327 MAG coverage software Reads (ERR7738515) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567081) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 80 Number of CRISPR spacer hits supporting host taxonomy 80 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_60_length_203813_cov_29.903797_1 Viral contig found in MAG ERR7738515_bin.61 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787338 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_60_length_203813_cov_29.903797_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0298777 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140277 SAMEA13538308 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738515. BACPHLIP temperate score 0.07381662166094104 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538308 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 9.16515 MAG coverage software Reads (ERR7738515) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567081) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_1562_length_22330_cov_5.229003 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787338 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_1562_length_22330_cov_5.229003 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738515_virus.1562 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140278 SAMEA13538309 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738515. BACPHLIP temperate score 0.17820990407225873 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538309 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 118.597 MAG coverage software Reads (ERR7738515) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567081) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_2432_length_13181_cov_69.728098 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; ITR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787338 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_2432_length_13181_cov_69.728098 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738515_virus.2432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140279 SAMEA13538310 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738515. BACPHLIP temperate score 0.275 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538310 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 10.9931 MAG coverage software Reads (ERR7738515) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567081) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_927_length_40172_cov_6.370271 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6511627906976745 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787338 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_11_CHE0005SZ__NODE_927_length_40172_cov_6.370271 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738515_virus.927 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140280 SAMEA13538311 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738527. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538311 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 201.062 MAG coverage software Reads (ERR7738527) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559349) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-I-L_K_10_2622__NODE_20_length_223125_cov_142.938448_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586331 sample name Hadza_MoBio_hadza-I-L_K_10_2622__NODE_20_length_223125_cov_142.938448_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738569_provirus.178 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140281 SAMEA13538312 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738527. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538312 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 390.845 MAG coverage software Reads (ERR7738527) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559349) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 150 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_MoBio_hadza-I-L_K_10_2622__NODE_685_length_51687_cov_222.612711_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586331 sample name Hadza_MoBio_hadza-I-L_K_10_2622__NODE_685_length_51687_cov_222.612711_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140282 SAMEA13538313 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738527. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538313 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 34.4824 MAG coverage software Reads (ERR7738527) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559349) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 1020 Submitter Id Hadza_MoBio_hadza-I-L_K_10_2622__NODE_1111_length_38808_cov_20.235419 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586331 sample name Hadza_MoBio_hadza-I-L_K_10_2622__NODE_1111_length_38808_cov_20.235419 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738527_virus.1111 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140283 SAMEA13538314 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738527. BACPHLIP temperate score 0.4875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538314 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 644.333 MAG coverage software Reads (ERR7738527) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559349) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_K_10_2622__NODE_1412_length_32870_cov_369.054890 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586331 sample name Hadza_MoBio_hadza-I-L_K_10_2622__NODE_1412_length_32870_cov_369.054890 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.1563 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140284 SAMEA13538315 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738527. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538315 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 14.5777 MAG coverage software Reads (ERR7738527) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559349) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_K_10_2622__NODE_23_length_219699_cov_8.439036 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 92.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9347826086956522 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586331 sample name Hadza_MoBio_hadza-I-L_K_10_2622__NODE_23_length_219699_cov_8.439036 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098563 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia sp900552665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738527_virus.23 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140285 SAMEA13538316 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738527. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538316 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 22.9802 MAG coverage software Reads (ERR7738527) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559349) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2385 Number of CRISPR spacer hits supporting host taxonomy 699 Submitter Id Hadza_MoBio_hadza-I-L_K_10_2622__NODE_453_length_64984_cov_13.512672 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5116279069767442 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586331 sample name Hadza_MoBio_hadza-I-L_K_10_2622__NODE_453_length_64984_cov_13.512672 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373893 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140286 SAMEA13538317 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738527. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538317 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 13.5485 MAG coverage software Reads (ERR7738527) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559349) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-I-L_K_10_2622__NODE_851_length_45846_cov_7.707378 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47368421052631576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586331 sample name Hadza_MoBio_hadza-I-L_K_10_2622__NODE_851_length_45846_cov_7.707378 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745859_virus.1405 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140287 SAMEA13538318 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738529. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538318 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 60.7417 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 686 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1189_length_52138_cov_36.589174_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1189_length_52138_cov_36.589174_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0369449 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140288 SAMEA13538319 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738529. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538319 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 285.002 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 204 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_172_length_158038_cov_170.620191_1 Viral contig found in MAG ERR7738529_bin.144 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_172_length_158038_cov_170.620191_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737972_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115;s__RUG115 sp900066395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_provirus.6 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140289 SAMEA13538320 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738529. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538320 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 199.916 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 225 Number of CRISPR spacer hits supporting host taxonomy 134 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_342_length_115702_cov_124.209505_1 Viral contig found in MAG ERR7738529_bin.96 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_342_length_115702_cov_124.209505_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268072 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella stercorea vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0318509 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140290 SAMEA13538321 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738529. BACPHLIP temperate score 0.10049472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538321 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 10.4561 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_736_length_74410_cov_6.277199_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_736_length_74410_cov_6.277199_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_provirus.996 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140291 SAMEA13538322 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738529. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538322 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 12.41 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 302 Number of CRISPR spacer hits supporting host taxonomy 139 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1133_length_53864_cov_7.421124 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1133_length_53864_cov_7.421124 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140292 SAMEA13538323 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738529. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538323 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 48.8302 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1575_length_41105_cov_29.375012 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1575_length_41105_cov_29.375012 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_virus.1575 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140293 SAMEA13538324 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738529. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538324 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 33.8984 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 389 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1959_length_34250_cov_20.525883 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_1959_length_34250_cov_20.525883 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_virus.1959 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140294 SAMEA13538325 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738529. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538325 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 21.2091 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 257 Number of CRISPR spacer hits supporting host taxonomy 867 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_2575_length_26430_cov_12.349865 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_2575_length_26430_cov_12.349865 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11140295 SAMEA13538326 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738529. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538326 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 13.3571 MAG coverage software Reads (ERR7738529) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 157 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_452_length_100217_cov_8.024665 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2608695652173913 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787391 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_5_RAU1020YZ__NODE_452_length_100217_cov_8.024665 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_virus.452 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140296 SAMEA13538327 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus provirus assembled from ERR7738530. BACPHLIP temperate score 0.9144553881807648 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538327 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 387.658 MAG coverage software Reads (ERR7738530) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560656) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 308 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Hadza_MoBio_hadza-E-H_E_13_1725__NODE_13_length_278863_cov_237.909041_1 Viral contig found in MAG ERR7738530_bin.25 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585968 sample name Hadza_MoBio_hadza-E-H_E_13_1725__NODE_13_length_278863_cov_237.909041_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738530_provirus.13 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11140297 SAMEA13538328 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738530. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538328 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 124.896 MAG coverage software Reads (ERR7738530) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560656) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 102 Submitter Id Hadza_MoBio_hadza-E-H_E_13_1725__NODE_4_length_494412_cov_78.509873_1 Viral contig found in MAG ERR7738530_bin.14 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585968 sample name Hadza_MoBio_hadza-E-H_E_13_1725__NODE_4_length_494412_cov_78.509873_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738530_provirus.4 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140298 SAMEA13538329 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738530. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538329 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 7.2447 MAG coverage software Reads (ERR7738530) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560656) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_E_13_1725__NODE_376_length_65402_cov_4.060390 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585968 sample name Hadza_MoBio_hadza-E-H_E_13_1725__NODE_376_length_65402_cov_4.060390 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738530_virus.376 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140299 SAMEA13538330 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738530. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538330 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 38.8886 MAG coverage software Reads (ERR7738530) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560656) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_E_13_1725__NODE_980_length_30771_cov_22.693686 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585968 sample name Hadza_MoBio_hadza-E-H_E_13_1725__NODE_980_length_30771_cov_22.693686 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME089567 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp001556435 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.2344 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140300 SAMEA13538331 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738531. BACPHLIP temperate score 0.17563694053537307 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538331 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 11.5342 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1680_length_39854_cov_7.573522_1 Viral contig found in MAG ERR7738531_bin.80 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1680_length_39854_cov_7.573522_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_provirus.210 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140301 SAMEA13538332 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738531. BACPHLIP temperate score 0.10658093884155775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538332 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 31.9618 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_3213_length_27586_cov_20.832637_1 Viral contig found in MAG ERR7738531_bin.73 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_3213_length_27586_cov_20.832637_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738531_provirus.3213 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140302 SAMEA13538333 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738531. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538333 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 18.9375 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_544_length_71578_cov_11.847261_1 Viral contig found in MAG ERR7738531_bin.167 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_544_length_71578_cov_11.847261_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746739_provirus.59 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140303 SAMEA13538334 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738531. BACPHLIP temperate score 0.07995594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538334 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 18.8555 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_97_length_155930_cov_11.541549_1 Viral contig found in MAG ERR7738531_bin.191 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_97_length_155930_cov_11.541549_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0323692 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140304 SAMEA13538335 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738531. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538335 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:55Z INSDC last update 2022-12-27T00:30:55Z INSDC status public MAG coverage depth 42.027 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1361_length_44759_cov_26.588000 Viral contig found in MAG ERR7738531_bin.161 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9655172413793104 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1361_length_44759_cov_26.588000 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_virus.1549 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140305 SAMEA13538336 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738531. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538336 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 54.8498 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1679_length_39854_cov_35.175906 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_1679_length_39854_cov_35.175906 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.1477 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140306 SAMEA13538337 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738531. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538337 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 10.1882 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 61 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_2045_length_35835_cov_6.184266 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_2045_length_35835_cov_6.184266 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140307 SAMEA13538338 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738531. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538338 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 11.3382 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 404 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_2623_length_30982_cov_6.952823 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.55 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_2623_length_30982_cov_6.952823 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_virus.1289 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140308 SAMEA13538339 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738531. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538339 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 41.7603 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 231 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_349_length_88584_cov_25.814670 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.41379310344827586 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_349_length_88584_cov_25.814670 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_virus.382 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11140309 SAMEA13538340 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738531. BACPHLIP temperate score 4.9472295514511e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538340 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 7.9528 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_4267_length_23051_cov_4.795682 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_4267_length_23051_cov_4.795682 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738273_bin.44 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_F;s__Ruminococcus_F champanellensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745582_virus.1597 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140310 SAMEA13538341 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738531. BACPHLIP temperate score 0.3875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538341 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 11.697 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_5614_length_19077_cov_7.581947 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_5614_length_19077_cov_7.581947 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747083_virus.1639 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140311 SAMEA13538342 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738531. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538342 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 17.74 MAG coverage software Reads (ERR7738531) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_960_length_53832_cov_11.123003 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585785 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_10_1530__NODE_960_length_53832_cov_11.123003 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738531_virus.960 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140312 SAMEA13538343 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738532. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538343 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:17Z INSDC last update 2022-12-27T19:09:17Z INSDC status public MAG coverage depth 71.7625 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 100 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_255_length_104894_cov_45.798716_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5161290322580645 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_255_length_104894_cov_45.798716_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_provirus.255 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140313 SAMEA13538344 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738532. BACPHLIP temperate score 0.20847882985254676 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538344 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 9.39895 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_820_length_56786_cov_5.511153_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_820_length_56786_cov_5.511153_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.526 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140314 SAMEA13538345 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738532. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538345 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 86.7808 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1240_length_44281_cov_50.348317 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.56 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1240_length_44281_cov_50.348317 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.1240 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140315 SAMEA13538346 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738532. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538346 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 82.3575 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1369_length_42373_cov_48.667936 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1369_length_42373_cov_48.667936 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746398_bin.161 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;s__Oribacterium sp900772695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140316 SAMEA13538347 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738532. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538347 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 16.4678 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 485 Number of CRISPR spacer hits supporting host taxonomy 1979 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1577_length_38751_cov_9.567410 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1577_length_38751_cov_9.567410 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0339015 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140317 SAMEA13538348 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738532. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538348 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 20.8658 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1811_length_35847_cov_12.310092 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_1811_length_35847_cov_12.310092 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.1811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140318 SAMEA13538349 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738532. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538349 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 175.473 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 247 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_2034_length_32962_cov_106.362171 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_2034_length_32962_cov_106.362171 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME256853 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302;s__CAG-302 sp001916775 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.2034 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140319 SAMEA13538350 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738532. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538350 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 33.8736 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_2455_length_28943_cov_21.210421 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_2455_length_28943_cov_21.210421 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.227 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140320 SAMEA13538351 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738532. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538351 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 11.5605 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_3054_length_24562_cov_6.655993 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_3054_length_24562_cov_6.655993 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R;s__Eubacterium_R sp900542875 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.3054 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140321 SAMEA13538352 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738532. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538352 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 16.6905 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_403_length_81558_cov_9.782563 Viral contig found in MAG ERR7738532_bin.116 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_403_length_81558_cov_9.782563 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.403 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140322 SAMEA13538353 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738532. BACPHLIP temperate score 0.24245594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538353 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 31.8139 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_467_length_75590_cov_19.452598 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_467_length_75590_cov_19.452598 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.467 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140323 SAMEA13538354 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738532. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538354 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 69.012200000000007 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_63_length_197736_cov_79.432841 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_63_length_197736_cov_79.432841 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp003514385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.62 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140324 SAMEA13538355 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738532. BACPHLIP temperate score 0.08284611230643936 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538355 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 6.7801 MAG coverage software Reads (ERR7738532) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560754) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_3_1732__NODE_8805_length_10500_cov_3.812818 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585975 sample name Hadza_MoBio_hadza-E-H_G_3_1732__NODE_8805_length_10500_cov_3.812818 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.8805 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140325 SAMEA13538356 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738533. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538356 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 224.971 MAG coverage software Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 99 Number of CRISPR spacer hits supporting host taxonomy 156 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_161_length_116745_cov_132.680992_1 Viral contig found in MAG ERR7738533_bin.22 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787388 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_161_length_116745_cov_132.680992_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.1094 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140326 SAMEA13538357 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis provirus assembled from ERR7738533. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538357 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 13.284 MAG coverage software Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_275_length_87636_cov_7.805423_1 Viral contig found in MAG ERR7738533_bin.36 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6739130434782609 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787388 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_275_length_87636_cov_7.805423_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_provirus.582 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11140327 SAMEA13538358 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738533. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538358 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 12.1112 MAG coverage software Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 104 Number of CRISPR spacer hits supporting host taxonomy 1653 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_727_length_48504_cov_7.135420_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6744186046511628 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787388 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_727_length_48504_cov_7.135420_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0362748 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140328 SAMEA13538359 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738533. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538359 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 615.891 MAG coverage software Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_206_length_103487_cov_360.607253 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787388 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_206_length_103487_cov_360.607253 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738533_virus.206 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140329 SAMEA13538360 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738533. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538360 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 936.188 MAG coverage software Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2758 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_747_length_47756_cov_631.610646 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787388 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_747_length_47756_cov_631.610646 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738533_virus.747 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140330 SAMEA13538361 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738533. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538361 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 14.4274 MAG coverage software Reads (ERR7738533) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 367 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_956_length_39684_cov_8.413235 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787388 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_13_RAU1011YZ__NODE_956_length_39684_cov_8.413235 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738533_virus.956 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140331 SAMEA13538362 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738534. BACPHLIP temperate score 0.12339347995716636 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538362 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 21.03 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_179_length_122435_cov_12.194348_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_179_length_122435_cov_12.194348_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745388_virus.661 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140332 SAMEA13538363 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738534. BACPHLIP temperate score 0.927477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538363 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 28.8985 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_53_length_213706_cov_16.614743_1 Viral contig found in MAG ERR7738534_bin.42 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9428571428571428 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_53_length_213706_cov_16.614743_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745625_virus.169 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140333 SAMEA13538364 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738534. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538364 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 55.5125 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_1065_length_46811_cov_31.693671 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_1065_length_46811_cov_31.693671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738534_virus.1065 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140334 SAMEA13538365 340016 uncultured virus This sample represents an uncultured Inovirus sp. virus assembled from ERR7738534. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538365 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 8.94587 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_13486_length_6283_cov_5.111988 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_13486_length_6283_cov_5.111988 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745431_virus.9041 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae; Inovirus; unclassified Inovirus; Inovirus sp. virus enrichment approach none ERS11140335 SAMEA13538366 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738534. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538366 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 7.98818 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 289 Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_1651_length_35083_cov_4.307490 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7931034482758621 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_1651_length_35083_cov_4.307490 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0272411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140336 SAMEA13538367 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade sp. virus assembled from ERR7738534. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538367 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 3812.99 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_239_length_104399_cov_2150.153745 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5161290322580645 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_239_length_104399_cov_2150.153745 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.558 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; UAG-readthrough crAss clade sp. virus enrichment approach none ERS11140337 SAMEA13538368 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738534. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538368 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 483.598 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_303_length_94037_cov_276.710260 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7317073170731707 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_303_length_94037_cov_276.710260 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.95 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140338 SAMEA13538369 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738534. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538369 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 27.4595 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_5038_length_14510_cov_15.629876 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_5038_length_14510_cov_15.629876 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_virus.6384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11140339 SAMEA13538370 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738534. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538370 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 25.943 MAG coverage software Reads (ERR7738534) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561146) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_3_1599__NODE_952_length_50310_cov_15.179782 Viral contig found in MAG ERR7738534_bin.233 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585848 sample name Hadza_MoBio_hadza-A-D_B_3_1599__NODE_952_length_50310_cov_15.179782 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738227_virus.620 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140340 SAMEA13538371 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738535. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538371 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 149.204 MAG coverage software Reads (ERR7738535) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_22_length_355978_cov_87.787882_1 Viral contig found in MAG ERR7738535_bin.103 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787401 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_22_length_355978_cov_87.787882_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738155_virus.49 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140341 SAMEA13538372 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus provirus assembled from ERR7738535. BACPHLIP temperate score 0.5375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538372 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 21.388 MAG coverage software Reads (ERR7738535) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 96 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_417_length_99601_cov_12.156565_1 Viral contig found in MAG ERR7738535_bin.95 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787401 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_417_length_99601_cov_12.156565_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__Bilophila wadsworthia vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738535_provirus.417 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11140342 SAMEA13538373 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738535. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538373 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 40.2529 MAG coverage software Reads (ERR7738535) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 106 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_8_length_460434_cov_24.912470_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787401 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_8_length_460434_cov_24.912470_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127;s__CAG-127 sp900319515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0351633 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140343 SAMEA13538374 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738535. BACPHLIP temperate score 0.5375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538374 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 145.357 MAG coverage software Reads (ERR7738535) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_1006_length_53691_cov_87.435465 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7567567567567568 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787401 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_1006_length_53691_cov_87.435465 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0320321 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140344 SAMEA13538375 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738535. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538375 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 43.1989 MAG coverage software Reads (ERR7738535) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 191 Number of CRISPR spacer hits supporting host taxonomy 247 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_1607_length_35393_cov_26.274635 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787401 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_1607_length_35393_cov_26.274635 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127;s__CAG-127 sp900319515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0352626 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140345 SAMEA13538376 336724 Myoviridae environmental samples This sample represents an uncultured Pbunavirus virus assembled from ERR7738535. BACPHLIP temperate score 0.17325395693569484 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538376 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 185.156 MAG coverage software Reads (ERR7738535) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1161 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_2077_length_27742_cov_106.553985 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.36585365853658536 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787401 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_2077_length_27742_cov_106.553985 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0277945 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Pbunavirus virus enrichment approach none ERS11140346 SAMEA13538377 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738535. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538377 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 60.2298 MAG coverage software Reads (ERR7738535) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 473 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_9057_length_6237_cov_36.506981 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787401 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_5_THA1056YZ__NODE_9057_length_6237_cov_36.506981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola dorei vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738535_virus.9057 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140347 SAMEA13538378 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738536. BACPHLIP temperate score 0.2095814977973569 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538378 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 16.3536 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 142 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_188_length_131773_cov_9.263167_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_188_length_131773_cov_9.263167_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140348 SAMEA13538379 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738536. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538379 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 14.0545 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_385_length_93487_cov_8.367091_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_385_length_93487_cov_8.367091_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.1152 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140349 SAMEA13538380 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738536. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538380 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 14.2002 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 166 Number of CRISPR spacer hits supporting host taxonomy 403 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_761_length_63903_cov_8.056356_1 Viral contig found in MAG ERR7738536_bin.114 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8484848484848485 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_761_length_63903_cov_8.056356_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_provirus.761 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140350 SAMEA13538381 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738536. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538381 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 132.682 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_12639_length_8654_cov_79.137461 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_12639_length_8654_cov_79.137461 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128517 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900290275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.12639 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140351 SAMEA13538382 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738536. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538382 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 17.7892 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 114 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_1530_length_42556_cov_10.084865 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7073170731707317 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_1530_length_42556_cov_10.084865 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745823_bin.49 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001;s__SFJ001 sp004555865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.1530 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140352 SAMEA13538383 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738536. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538383 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 8.78916 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_1666_length_40521_cov_4.910790 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_1666_length_40521_cov_4.910790 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.1666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140353 SAMEA13538384 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738536. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538384 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 313.974 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_207_length_127831_cov_189.135166 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_207_length_127831_cov_189.135166 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738204_virus.53 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140354 SAMEA13538385 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738536. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538385 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 542.677 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_302_length_105790_cov_298.920540 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9801980198019802 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_302_length_105790_cov_298.920540 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745577_virus.211 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11140355 SAMEA13538386 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738536. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538386 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 31.5083 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 189 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_465_length_85546_cov_18.675578 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_465_length_85546_cov_18.675578 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.465 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140356 SAMEA13538387 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738536. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538387 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 70.667 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_65_length_200591_cov_39.827583 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 84.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_65_length_200591_cov_39.827583 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.65 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140357 SAMEA13538388 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738536. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538388 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 10.8634 MAG coverage software Reads (ERR7738536) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_G_15_1738__NODE_859_length_59906_cov_6.093266 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9574468085106383 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585981 sample name Hadza_MoBio_hadza-E-H_G_15_1738__NODE_859_length_59906_cov_6.093266 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_virus.859 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140358 SAMEA13538389 336724 Myoviridae environmental samples This sample represents an uncultured Bacillus virus 125 provirus assembled from ERR7738537. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538389 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:05Z INSDC last update 2022-12-27T00:31:05Z INSDC status public MAG coverage depth 19.1596 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_11_length_407929_cov_11.321112_1 Viral contig found in MAG ERR7738537_bin.54 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_11_length_407929_cov_11.321112_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.1424 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Elmenteitavirus; Bacillus virus 125 virus enrichment approach none ERS11140359 SAMEA13538390 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738537. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538390 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 21.2343 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 100 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_186_length_147341_cov_12.610509_1 Viral contig found in MAG ERR7738537_bin.160 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_186_length_147341_cov_12.610509_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140360 SAMEA13538391 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738537. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538391 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 23.2453 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 131 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_378_length_109472_cov_14.108149_1 Viral contig found in MAG ERR7738537_bin.114 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_378_length_109472_cov_14.108149_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0354042 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140361 SAMEA13538392 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738537. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538392 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 15.2582 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_765_length_74244_cov_8.812787_1 Viral contig found in MAG ERR7738537_bin.133 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_765_length_74244_cov_8.812787_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME006546 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-605;s__CAG-605 sp000433255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.165 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140362 SAMEA13538393 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738537. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538393 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 200.49 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_11501_length_10722_cov_119.101861 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_11501_length_10722_cov_119.101861 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.12584 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11140363 SAMEA13538394 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738537. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538394 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 16.3672 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_1670_length_46996_cov_9.889171 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_1670_length_46996_cov_9.889171 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.386 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140364 SAMEA13538395 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738537. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538395 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 9.02169 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_1997_length_41510_cov_5.000121 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_1997_length_41510_cov_5.000121 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.2031 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140365 SAMEA13538396 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738537. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538396 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 11.7092 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_2336_length_37345_cov_6.979151 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_2336_length_37345_cov_6.979151 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.1832 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140366 SAMEA13538397 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738537. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538397 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 10.6604 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_2613_length_34450_cov_6.205277 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_2613_length_34450_cov_6.205277 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738537_virus.2613 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140367 SAMEA13538398 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738537. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538398 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 11.5934 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 200 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_3351_length_28612_cov_7.044437 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_3351_length_28612_cov_7.044437 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000448 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900066885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.3815 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140368 SAMEA13538399 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738537. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538399 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 11.683 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 159 Number of CRISPR spacer hits supporting host taxonomy 964 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_4012_length_24840_cov_6.938134 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_4012_length_24840_cov_6.938134 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738145_provirus.803 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140369 SAMEA13538400 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738537. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538400 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 18.5064 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 249 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_455_length_99305_cov_11.283378 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9032258064516128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_455_length_99305_cov_11.283378 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.582 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140370 SAMEA13538401 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738537. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538401 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 34.2914 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 242 Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_545_length_90932_cov_20.621507 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_545_length_90932_cov_20.621507 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.604 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140371 SAMEA13538402 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738537. BACPHLIP temperate score 0.03729583153820042 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538402 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 13.2792 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_7333_length_15381_cov_7.649765 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_7333_length_15381_cov_7.649765 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.10576 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140372 SAMEA13538403 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738537. BACPHLIP temperate score 0.12578965839962564 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538403 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 23.2413 MAG coverage software Reads (ERR7738537) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_6_2213__NODE_977_length_63895_cov_13.404823 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586156 sample name Hadza_MoBio_hadza-E-H_F_6_2213__NODE_977_length_63895_cov_13.404823 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.1218 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140373 SAMEA13538404 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738544. BACPHLIP temperate score 0.04493392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538404 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 104.355 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_204_length_114886_cov_67.193704_1 Viral contig found in MAG ERR7738544_bin.144 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_204_length_114886_cov_67.193704_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_provirus.204 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140374 SAMEA13538405 2133760 Siphoviridae environmental samples This sample represents an uncultured Psavirus provirus assembled from ERR7738544. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538405 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 69.4072 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_335_length_89948_cov_45.781743_1 Viral contig found in MAG ERR7738544_bin.14 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_335_length_89948_cov_45.781743_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME261291 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;s__NK3B98 sp900545815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0194573 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Psavirus virus enrichment approach none ERS11140375 SAMEA13538406 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738544. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538406 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 22.8606 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1083_length_45487_cov_14.042348 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1083_length_45487_cov_14.042348 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0316936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140376 SAMEA13538407 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738544. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538407 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 45.309 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1275_length_41237_cov_25.864942 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1275_length_41237_cov_25.864942 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_virus.1275 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140377 SAMEA13538408 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738544. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538408 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 16.668 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1449_length_38203_cov_10.183182 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1449_length_38203_cov_10.183182 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_virus.1449 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140378 SAMEA13538409 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738544. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538409 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 74.0202 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1676_length_34288_cov_43.281225 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_1676_length_34288_cov_43.281225 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_virus.1676 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140379 SAMEA13538410 2133760 Siphoviridae environmental samples This sample represents an uncultured unclassified Uwajimavirus virus assembled from ERR7738544. BACPHLIP temperate score 0.16349074572837724 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538410 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 12.3185 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_2203_length_28636_cov_6.921811 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5652173913043478 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_2203_length_28636_cov_6.921811 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_virus.2203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Uwajimavirus; unclassified Uwajimavirus virus enrichment approach none ERS11140380 SAMEA13538411 2133760 Siphoviridae environmental samples This sample represents an uncultured Lactobacillus phage JNU_P7 virus assembled from ERR7738544. BACPHLIP temperate score 0.3625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538411 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 8.61906 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_3130_length_22319_cov_4.972215 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_3130_length_22319_cov_4.972215 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142482 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus paragasseri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_virus.3130 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lactobacillus phage JNU_P7 virus enrichment approach none ERS11140381 SAMEA13538412 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738544. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538412 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 169.587 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_4516_length_17014_cov_97.736671 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_4516_length_17014_cov_97.736671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_virus.4516 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140382 SAMEA13538413 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738544. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538413 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 117.952 MAG coverage software Reads (ERR7738544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560311) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-E-H_I_1_1742__NODE_678_length_61032_cov_66.650808 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9655172413793104 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585985 sample name Hadza_MoBio_hadza-E-H_I_1_1742__NODE_678_length_61032_cov_66.650808 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME111561 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_virus.678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140383 SAMEA13538414 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738545. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538414 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 59.8792 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 100 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_204_length_102130_cov_33.497036_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4482758620689655 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_204_length_102130_cov_33.497036_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_provirus.688 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140384 SAMEA13538415 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738545. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538415 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 8.96609 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 523 Number of CRISPR spacer hits supporting host taxonomy 1798 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_650_length_53408_cov_4.869607_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7575757575757576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_650_length_53408_cov_4.869607_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0339015 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140385 SAMEA13538416 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738545. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538416 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 12.2907 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_1055_length_39144_cov_6.816828 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7741935483870968 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_1055_length_39144_cov_6.816828 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738545_virus.1055 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140386 SAMEA13538417 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738545. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538417 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 12.2689 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_1272_length_33989_cov_6.580886 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_1272_length_33989_cov_6.580886 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738545_virus.1272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140387 SAMEA13538418 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738545. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538418 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 121.13 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_1699_length_27338_cov_68.365504 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_1699_length_27338_cov_68.365504 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0299046 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140388 SAMEA13538419 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738545. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538419 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 476.283 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 625 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_294_length_84465_cov_264.370456 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3888888888888889 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_294_length_84465_cov_264.370456 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738545_virus.294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140389 SAMEA13538420 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738545. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538420 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 45.1276 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_472_length_64237_cov_25.182700 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_472_length_64237_cov_25.182700 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0358019 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140390 SAMEA13538421 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738545. BACPHLIP temperate score 0.01734581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538421 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 116.278 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_747_length_49139_cov_64.623476 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_747_length_49139_cov_64.623476 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738545_virus.747 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140391 SAMEA13538422 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738545. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538422 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 9.41964 MAG coverage software Reads (ERR7738545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_911_length_42710_cov_5.097389 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787348 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_21_CHE1011TZ__NODE_911_length_42710_cov_5.097389 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738545_virus.911 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140392 SAMEA13538423 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738546. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538423 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 17.6303 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_138_length_193508_cov_9.691942_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_138_length_193508_cov_9.691942_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143232 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides cellulosilyticus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738546_provirus.138 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140393 SAMEA13538424 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738546. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538424 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 116.479 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_1848_length_42788_cov_73.855026_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_1848_length_42788_cov_73.855026_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738546_provirus.1848 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140394 SAMEA13538425 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738546. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538425 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 17.7053 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_415_length_112319_cov_9.724453_1 Viral contig found in MAG ERR7738546_bin.209 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9722222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_415_length_112319_cov_9.724453_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738546_provirus.415 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140395 SAMEA13538426 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738546. BACPHLIP temperate score 0.10236784140969166 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538426 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 10.7119 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_681_length_84342_cov_5.797057_1 Viral contig found in MAG ERR7738546_bin.12 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_681_length_84342_cov_5.797057_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001239 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G;s__Eubacterium_G ventriosum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0261300 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140396 SAMEA13538427 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738546. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538427 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 3252.18 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 555 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_940_length_68410_cov_1838.652159_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5652173913043478 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_940_length_68410_cov_1838.652159_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140397 SAMEA13538428 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738546. BACPHLIP temperate score 0.4625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538428 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 77.058 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_121_length_204103_cov_45.262354 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.54 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_121_length_204103_cov_45.262354 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola dorei vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380260 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140398 SAMEA13538429 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738546. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538429 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 17.0004 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 511 Number of CRISPR spacer hits supporting host taxonomy 1903 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_1474_length_50658_cov_9.382495 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9295774647887324 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_1474_length_50658_cov_9.382495 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0371591 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11140399 SAMEA13538430 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738546. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538430 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 9.05957 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_1749_length_44716_cov_4.893501 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_1749_length_44716_cov_4.893501 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738546_virus.1749 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140400 SAMEA13538431 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738546. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538431 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 21.3006 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 476 Number of CRISPR spacer hits supporting host taxonomy 1808 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_2127_length_38397_cov_12.177427 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6774193548387096 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_2127_length_38397_cov_12.177427 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738662_provirus.55 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140401 SAMEA13538432 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738546. BACPHLIP temperate score 0.12241189427312778 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538432 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 14.5771 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 272 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_2707_length_30867_cov_7.855732 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8787878787878788 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_2707_length_30867_cov_7.855732 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372952 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11140402 SAMEA13538433 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738546. BACPHLIP temperate score 0.05236784140969162 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538433 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 8.01884 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_4162_length_20528_cov_4.301061 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_4162_length_20528_cov_4.301061 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0342086 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140403 SAMEA13538434 1701671 uncultured podovirus This sample represents an uncultured CrAss-like virus sp. virus assembled from ERR7738546. BACPHLIP temperate score 0.17233342861947878 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538434 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 146.508 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_584_length_92079_cov_80.226104 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.986842105263158 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_584_length_92079_cov_80.226104 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0362043 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; CrAss-like virus sp. virus enrichment approach none ERS11140404 SAMEA13538435 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738546. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538435 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 88.6684 MAG coverage software Reads (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1961 Number of CRISPR spacer hits supporting host taxonomy 380 Submitter Id Pilot_MoBio_Fiber_C_4_7003__NODE_888_length_70890_cov_48.830624 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.9791666666666666 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383897 sample name Pilot_MoBio_Fiber_C_4_7003__NODE_888_length_70890_cov_48.830624 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0374335 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11140405 SAMEA13538436 336724 Myoviridae environmental samples This sample represents an uncultured Winogradskyella phage Peternella_1 provirus assembled from ERR7738547. BACPHLIP temperate score 0.1130538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538436 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 153.513 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 250 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_1291_length_53524_cov_94.982487_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5172413793103449 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_1291_length_53524_cov_94.982487_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0363290 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Winogradskyella phage Peternella_1 virus enrichment approach none ERS11140406 SAMEA13538437 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738547. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538437 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 30.4493 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_177_length_165483_cov_17.319420_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_177_length_165483_cov_17.319420_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738547_provirus.177 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140407 SAMEA13538438 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738547. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538438 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 21.9044 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 177 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_291_length_130090_cov_12.658765_1 Viral contig found in MAG ERR7738547_bin.123 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_291_length_130090_cov_12.658765_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001635 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter;s__Odoribacter splanchnicus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738547_provirus.291 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140408 SAMEA13538439 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus provirus assembled from ERR7738547. BACPHLIP temperate score 0.05830901147062301 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538439 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 71.988 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_681_length_83757_cov_42.879649_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_681_length_83757_cov_42.879649_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME058212 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp900539375 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738547_provirus.681 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11140409 SAMEA13538440 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738547. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538440 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 246.668 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 468 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_1197_length_56827_cov_141.017427 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.59375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_1197_length_56827_cov_141.017427 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738514_provirus.899 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140410 SAMEA13538441 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738547. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538441 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 32.0891 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 112 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_1453_length_48933_cov_18.370129 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_1453_length_48933_cov_18.370129 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140411 SAMEA13538442 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738547. BACPHLIP temperate score 4.9472295514511e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538442 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 41.9184 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_1826_length_41105_cov_24.972238 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_1826_length_41105_cov_24.972238 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0285998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140412 SAMEA13538443 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738547. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538443 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 9.17049 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_3234_length_24192_cov_5.186481 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_3234_length_24192_cov_5.186481 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738665_bin.322 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1623;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738547_virus.3234 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140413 SAMEA13538444 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738547. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538444 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 17.7627 MAG coverage software Reads (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Pilot_MoBio_Fiber_G_11_1024__NODE_5919_length_12334_cov_10.268230 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384077 sample name Pilot_MoBio_Fiber_G_11_1024__NODE_5919_length_12334_cov_10.268230 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME104932 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I;s__Eubacterium_I ramulus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738547_virus.5919 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140414 SAMEA13538445 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738548. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538445 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 9.66751 MAG coverage software Reads (ERR7738548) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567341) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_448_length_47763_cov_5.788722_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787392 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_448_length_47763_cov_5.788722_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738548_provirus.448 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140415 SAMEA13538446 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738548. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538446 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 388.331 MAG coverage software Reads (ERR7738548) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567341) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_234_length_68576_cov_236.183302 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4230769230769231 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787392 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_234_length_68576_cov_236.183302 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738548_virus.234 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140416 SAMEA13538447 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738548. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538447 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 81.8343 MAG coverage software Reads (ERR7738548) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567341) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_804_length_31948_cov_50.287722 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787392 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_804_length_31948_cov_50.287722 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738548_virus.804 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140417 SAMEA13538448 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738549. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538448 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 11.972 MAG coverage software Reads (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 941 Number of CRISPR spacer hits supporting host taxonomy 235 Submitter Id Pilot_MoBio_Fiber_N_24_7019__NODE_33_length_266230_cov_6.806115_1 Viral contig found in MAG ERR7738549_bin.12 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8620689655172413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383912 sample name Pilot_MoBio_Fiber_N_24_7019__NODE_33_length_266230_cov_6.806115_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738578_provirus.116 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140418 SAMEA13538449 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738549. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538449 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 2298.9 MAG coverage software Reads (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 219 Number of CRISPR spacer hits supporting host taxonomy 256 Submitter Id Pilot_MoBio_Fiber_N_24_7019__NODE_699_length_67491_cov_1332.446969_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383912 sample name Pilot_MoBio_Fiber_N_24_7019__NODE_699_length_67491_cov_1332.446969_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0308466 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140419 SAMEA13538450 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738549. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13538450 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-28T19:46:10Z INSDC status public MAG coverage depth 41.5781 MAG coverage software Reads (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 211 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Pilot_MoBio_Fiber_N_24_7019__NODE_1198_length_45294_cov_23.878475 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383912 sample name Pilot_MoBio_Fiber_N_24_7019__NODE_1198_length_45294_cov_23.878475 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738549_virus.1198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140420 SAMEA13538451 336724 Myoviridae environmental samples This sample represents an uncultured Winogradskyella phage Peternella_1 virus assembled from ERR7738549. BACPHLIP temperate score 0.275 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538451 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 245.137 MAG coverage software Reads (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1057 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Pilot_MoBio_Fiber_N_24_7019__NODE_1476_length_38070_cov_140.274314 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383912 sample name Pilot_MoBio_Fiber_N_24_7019__NODE_1476_length_38070_cov_140.274314 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745596_virus.306 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Winogradskyella phage Peternella_1 virus enrichment approach none ERS11140421 SAMEA13538452 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738549. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538452 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 23.8036 MAG coverage software Reads (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 110 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Pilot_MoBio_Fiber_N_24_7019__NODE_2018_length_28947_cov_13.875996 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383912 sample name Pilot_MoBio_Fiber_N_24_7019__NODE_2018_length_28947_cov_13.875996 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0278013 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140422 SAMEA13538453 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738549. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538453 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:07Z INSDC last update 2022-12-27T00:30:07Z INSDC status public MAG coverage depth 6.80592 MAG coverage software Reads (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_N_24_7019__NODE_3077_length_19724_cov_3.658828 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383912 sample name Pilot_MoBio_Fiber_N_24_7019__NODE_3077_length_19724_cov_3.658828 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001120 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides thetaiotaomicron vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0252096 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140423 SAMEA13538454 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738549. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538454 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 6.98737 MAG coverage software Reads (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 90 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_N_24_7019__NODE_6530_length_9256_cov_3.896394 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383912 sample name Pilot_MoBio_Fiber_N_24_7019__NODE_6530_length_9256_cov_3.896394 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738549_virus.6530 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140424 SAMEA13538455 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738550. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538455 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 31.2707 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 96 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_100_length_225077_cov_18.575009_1 Viral contig found in MAG ERR7738550_bin.27 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_100_length_225077_cov_18.575009_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140425 SAMEA13538456 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738550. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538456 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 459.461 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2062_length_43942_cov_269.247669_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2062_length_43942_cov_269.247669_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_virus.1626 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140426 SAMEA13538457 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738550. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538457 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 13.1496 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2772_length_35189_cov_7.520734_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2772_length_35189_cov_7.520734_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_provirus.2772 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140427 SAMEA13538458 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738550. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538458 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 20.6977 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_443_length_120084_cov_12.054563_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_443_length_120084_cov_12.054563_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_provirus.443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140428 SAMEA13538459 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738550. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538459 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 31.1177 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_775_length_87042_cov_18.294199_1 Viral contig found in MAG ERR7738550_bin.228 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_775_length_87042_cov_18.294199_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.29 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900554205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_provirus.327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140429 SAMEA13538460 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738550. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538460 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 87.6441 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_1189_length_64557_cov_51.531715 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_1189_length_64557_cov_51.531715 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738148_bin.20 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A;s__Selenomonas_A sp900769615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.1189 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140430 SAMEA13538461 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738550. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538461 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 7.41548 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 180 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_15544_length_8018_cov_4.182471 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_15544_length_8018_cov_4.182471 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0091843 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140431 SAMEA13538462 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738550. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538462 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 10.6333 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2100_length_43284_cov_6.033999 Viral contig found in MAG ERR7738550_bin.234 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2100_length_43284_cov_6.033999 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.2100 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140432 SAMEA13538463 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738550. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538463 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 24.1546 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2385_length_39154_cov_14.206515 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2385_length_39154_cov_14.206515 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.2385 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140433 SAMEA13538464 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738550. BACPHLIP temperate score 0.13986784140969166 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538464 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 17.2303 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2693_length_35944_cov_9.893746 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_2693_length_35944_cov_9.893746 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.2693 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140434 SAMEA13538465 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738550. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538465 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 106.579 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_3375_length_30075_cov_62.594340 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_3375_length_30075_cov_62.594340 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738574_virus.2447 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140435 SAMEA13538466 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738550. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538466 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 9.41739 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_4078_length_25630_cov_5.559386 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_4078_length_25630_cov_5.559386 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.4078 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140436 SAMEA13538467 2133760 Siphoviridae environmental samples This sample represents an uncultured Bacillus virus 250 virus assembled from ERR7738550. BACPHLIP temperate score 0.0490368859781216 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538467 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 6.12224 MAG coverage software Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_B_9_1942__NODE_6033_length_18262_cov_3.275282 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586081 sample name Hadza_MoBio_hadza-E-H_B_9_1942__NODE_6033_length_18262_cov_3.275282 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.110 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__HGM11416;s__HGM11416 sp900768525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.2426 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cecivirus; Bacillus virus 250 virus enrichment approach none ERS11140437 SAMEA13538468 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738551. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538468 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 21.1677 MAG coverage software Reads (ERR7738551) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567508) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_137_length_125099_cov_11.800355_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 12 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.851063829787234 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787409 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_137_length_125099_cov_11.800355_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738551_provirus.137 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140438 SAMEA13538469 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738551. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538469 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 17.0811 MAG coverage software Reads (ERR7738551) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567508) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_39_length_212087_cov_9.568303_1 Viral contig found in MAG ERR7738551_bin.65 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787409 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_39_length_212087_cov_9.568303_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738551_provirus.39 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140439 SAMEA13538470 2100421 uncultured Caudovirales phage This sample represents an uncultured Teseptimavirus virus assembled from ERR7738551. BACPHLIP temperate score 0.00270137614315428 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538470 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 820.947 MAG coverage software Reads (ERR7738551) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567508) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_1056_length_38916_cov_457.136435 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9607843137254902 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787409 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_1056_length_38916_cov_457.136435 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738551_virus.1056 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae; Studiervirinae; Teseptimavirus virus enrichment approach none ERS11140440 SAMEA13538471 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738551. BACPHLIP temperate score 0.8061536050499776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538471 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 994.239 MAG coverage software Reads (ERR7738551) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567508) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_1684_length_27097_cov_554.496040 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787409 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_1684_length_27097_cov_554.496040 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_virus.1079 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140441 SAMEA13538472 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738551. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538472 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 22.1176 MAG coverage software Reads (ERR7738551) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567508) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 236 Number of CRISPR spacer hits supporting host taxonomy 459 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_333_length_81901_cov_12.308870 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 11 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.7659574468085106 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787409 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_333_length_81901_cov_12.308870 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738653_provirus.102 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140442 SAMEA13538473 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738551. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538473 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 14.108 MAG coverage software Reads (ERR7738551) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567508) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 143 Number of CRISPR spacer hits supporting host taxonomy 368 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_814_length_46199_cov_8.075170 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787409 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_7_THA1071YZ__NODE_814_length_46199_cov_8.075170 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738548_provirus.10 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140443 SAMEA13538474 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738552. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538474 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 30.4946 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_1227_length_64074_cov_18.807819_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_1227_length_64074_cov_18.807819_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738273_bin.44 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_F;s__Ruminococcus_F champanellensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_provirus.1227 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140444 SAMEA13538475 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738552. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538475 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 27.1099 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 272 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_2364_length_41785_cov_17.169848_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.96 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_2364_length_41785_cov_17.169848_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_virus.2651 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140445 SAMEA13538476 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738552. BACPHLIP temperate score 0.02102144645966927 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538476 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 10.0377 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_338_length_131333_cov_5.757565_1 Viral contig found in MAG ERR7738552_bin.288 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_338_length_131333_cov_5.757565_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_provirus.1139 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140446 SAMEA13538477 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738552. BACPHLIP temperate score 0.02188930888561058 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538477 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 23.2402 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_495_length_107606_cov_14.041561_1 Viral contig found in MAG ERR7738552_bin.279 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_495_length_107606_cov_14.041561_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.2731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140447 SAMEA13538478 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738552. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538478 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 38.0645 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_638_length_92727_cov_23.137410_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5172413793103449 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_638_length_92727_cov_23.137410_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_provirus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140448 SAMEA13538479 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738552. BACPHLIP temperate score 0.09694350320639454 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538479 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 48.4925 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_10660_length_13000_cov_28.290051 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_10660_length_13000_cov_28.290051 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.3248703 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140449 SAMEA13538480 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738552. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538480 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 13.2706 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_1564_length_55085_cov_7.988947 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_1564_length_55085_cov_7.988947 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.1564 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11140450 SAMEA13538481 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738552. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538481 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 14.3957 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_1956_length_47854_cov_8.489043 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_1956_length_47854_cov_8.489043 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.274 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__W3P20-009;g__W3P20-009;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.1956 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140451 SAMEA13538482 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738552. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538482 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 79.223 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 114 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_2401_length_41429_cov_48.348157 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8620689655172413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_2401_length_41429_cov_48.348157 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738179_virus.1416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140452 SAMEA13538483 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738552. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538483 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 15.8224 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_272_length_145730_cov_9.488215 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 19 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.6949152542372882 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_272_length_145730_cov_9.488215 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140453 SAMEA13538484 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738552. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538484 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 15.8032 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_3010_length_35344_cov_9.746874 Viral contig found in MAG ERR7738552_bin.123 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_3010_length_35344_cov_9.746874 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.3010 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140454 SAMEA13538485 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738552. BACPHLIP temperate score 0.00495594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538485 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:08Z INSDC last update 2022-12-27T00:30:08Z INSDC status public MAG coverage depth 21.3431 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_3578_length_30999_cov_12.904631 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_3578_length_30999_cov_12.904631 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__CAG-238;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_virus.2180 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140455 SAMEA13538486 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738552. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538486 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 53.7958 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_501_length_106706_cov_31.921682 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9666666666666668 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_501_length_106706_cov_31.921682 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738531_virus.150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140456 SAMEA13538487 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738552. BACPHLIP temperate score 0.05484581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538487 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 7.46971 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_5627_length_21757_cov_4.348847 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_5627_length_21757_cov_4.348847 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_virus.2315 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140457 SAMEA13538488 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738552. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538488 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 54.7764 MAG coverage software Reads (ERR7738552) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_781_length_83271_cov_32.004399 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586159 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_4_2225__NODE_781_length_83271_cov_32.004399 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738268_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71;s__UBA71 sp002504495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.781 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140458 SAMEA13538489 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738553. BACPHLIP temperate score 0.11920980428964167 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538489 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:09Z INSDC last update 2022-12-27T00:30:09Z INSDC status public MAG coverage depth 335.976 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_136_length_159414_cov_187.430986_1 Viral contig found in MAG ERR7738553_bin.121 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_136_length_159414_cov_187.430986_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140459 SAMEA13538490 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. provirus assembled from ERR7738553. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538490 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 3.46397 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_24461_length_3730_cov_1.687106_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_24461_length_3730_cov_1.687106_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME079077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000434935 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_provirus.24461 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140460 SAMEA13538491 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738553. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538491 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 12.6706 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_412_length_92449_cov_7.059888_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_412_length_92449_cov_7.059888_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_provirus.412 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140461 SAMEA13538492 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738553. BACPHLIP temperate score 0.06622982580247963 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538492 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 19.0979 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 108 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_542_length_80248_cov_10.722917_1 Viral contig found in MAG ERR7738553_bin.8 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3928571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_542_length_80248_cov_10.722917_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_provirus.542 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140462 SAMEA13538493 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738553. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538493 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 212.294 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_812_length_63061_cov_123.865283_1 Viral contig found in MAG ERR7738553_bin.44 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_812_length_63061_cov_123.865283_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0352664 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140463 SAMEA13538494 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538494 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 11.1569 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1081_length_52980_cov_6.188307 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1081_length_52980_cov_6.188307 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.1081 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140464 SAMEA13538495 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538495 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 12.5066 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1245_length_48793_cov_6.962127 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1245_length_48793_cov_6.962127 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737972_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115;s__RUG115 sp900066395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.1245 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140465 SAMEA13538496 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7738553. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538496 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 37.9717 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_14365_length_6131_cov_20.677569 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_14365_length_6131_cov_20.677569 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000434975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.14365 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11140466 SAMEA13538497 926697 uncultured Microviridae This sample represents an uncultured unclassified Microviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538497 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 37.6178 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_15590_length_5671_cov_20.659814 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_15590_length_5671_cov_20.659814 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME232472 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-288;g__CAG-568;s__CAG-568 sp000434395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_virus.17697 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae virus enrichment approach none ERS11140467 SAMEA13538498 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538498 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 18.4194 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1662_length_39919_cov_10.271698 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1662_length_39919_cov_10.271698 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.284 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140468 SAMEA13538499 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.03243392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538499 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 151.481 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 67 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1791_length_37919_cov_85.677184 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1791_length_37919_cov_85.677184 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738144_virus.294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140469 SAMEA13538500 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738553. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538500 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 23.4094 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 360 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1931_length_35812_cov_13.119519 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_1931_length_35812_cov_13.119519 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.1347 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140470 SAMEA13538501 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538501 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 40.1968 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2038_length_34571_cov_22.685974 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7575757575757576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2038_length_34571_cov_22.685974 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME255646 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900552475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.2038 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140471 SAMEA13538502 2133760 Siphoviridae environmental samples This sample represents an uncultured Cecivirus virus assembled from ERR7738553. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538502 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 28.8934 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2173_length_32967_cov_16.476680 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2173_length_32967_cov_16.476680 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738273_bin.44 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_F;s__Ruminococcus_F champanellensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.2173 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cecivirus virus enrichment approach none ERS11140472 SAMEA13538503 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738553. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538503 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 70.534 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 282 Number of CRISPR spacer hits supporting host taxonomy 1145 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2445_length_30123_cov_39.250516 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2445_length_30123_cov_39.250516 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11140473 SAMEA13538504 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7738553. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538504 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 22.5957 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 319 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2653_length_28136_cov_12.718094 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_2653_length_28136_cov_12.718094 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.2653 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11140474 SAMEA13538505 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538505 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 36.8607 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_336_length_102363_cov_20.705678 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5853658536585366 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_336_length_102363_cov_20.705678 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746285_bin.189 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140475 SAMEA13538506 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738553. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538506 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 112.209 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_3691_length_21258_cov_63.131155 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_3691_length_21258_cov_63.131155 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745779_provirus.1128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140476 SAMEA13538507 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538507 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 12.6403 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_4549_length_17601_cov_7.120749 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_4549_length_17601_cov_7.120749 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.4549 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140477 SAMEA13538508 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538508 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 23.0661 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_61_length_238374_cov_12.978367 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8412698412698413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_61_length_238374_cov_12.978367 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140478 SAMEA13538509 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738553. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538509 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 171.157 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_849_length_61614_cov_96.326324 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_849_length_61614_cov_96.326324 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.849 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140479 SAMEA13538510 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738553. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538510 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 44.0626 MAG coverage software Reads (ERR7738553) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567226) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_99_length_187437_cov_24.798644 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5316455696202531 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787345 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_13_CHE1006Z__NODE_99_length_187437_cov_24.798644 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.80 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140480 SAMEA13538511 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738554. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538511 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 16.4126 MAG coverage software Reads (ERR7738554) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567414) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 167 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_339_length_76533_cov_9.479505_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787397 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_339_length_76533_cov_9.479505_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_provirus.339 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140481 SAMEA13538512 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738554. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538512 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 11.3696 MAG coverage software Reads (ERR7738554) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567414) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_772_length_46353_cov_6.428581_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787397 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_772_length_46353_cov_6.428581_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_provirus.772 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140482 SAMEA13538513 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738554. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538513 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 9.43181 MAG coverage software Reads (ERR7738554) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567414) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 320 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_1193_length_33771_cov_5.230961 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787397 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_1193_length_33771_cov_5.230961 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.1193 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11140483 SAMEA13538514 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738554. BACPHLIP temperate score 0.2544333617490467 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538514 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 19.7082 MAG coverage software Reads (ERR7738554) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567414) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 200 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_2153_length_21227_cov_15.587234 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787397 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_2153_length_21227_cov_15.587234 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME212098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.2153 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140484 SAMEA13538515 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738554. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538515 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 14.6578 MAG coverage software Reads (ERR7738554) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567414) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_535_length_59552_cov_8.396789 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787397 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_535_length_59552_cov_8.396789 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.535 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140485 SAMEA13538516 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738554. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538516 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 15.6893 MAG coverage software Reads (ERR7738554) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567414) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 444 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_967_length_39127_cov_8.964430 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.53125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787397 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_9_THA0062YZ__NODE_967_length_39127_cov_8.964430 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.967 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11140486 SAMEA13538517 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738555. BACPHLIP temperate score 0.852477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538517 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 289.17 MAG coverage software Reads (ERR7738555) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567620) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 613 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_175_length_124394_cov_167.965113_1 Viral contig found in MAG ERR7738555_bin.118 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_175_length_124394_cov_167.965113_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME108259 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900313215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738433_provirus.31 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140487 SAMEA13538518 1478972 Gokushovirinae environmental samples This sample represents an uncultured Gokushovirus WZ-2015a provirus assembled from ERR7738555. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538518 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 49.6568 MAG coverage software Reads (ERR7738555) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567620) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_393_length_84369_cov_31.195511_1_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_393_length_84369_cov_31.195511_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.5992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; unclassified Gokushovirinae; Gokushovirus WZ-2015a virus enrichment approach none ERS11140488 SAMEA13538519 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738555. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538519 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 78.401 MAG coverage software Reads (ERR7738555) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567620) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 525 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_1070_length_43175_cov_44.700172 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_1070_length_43175_cov_44.700172 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745366_virus.421 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140489 SAMEA13538520 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738555. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538520 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 7.04552 MAG coverage software Reads (ERR7738555) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567620) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_2076_length_24778_cov_3.700538 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_2076_length_24778_cov_3.700538 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492;s__CAG-492 sp000434335;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745366_virus.485 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140490 SAMEA13538521 2100421 uncultured Caudovirales phage This sample represents an uncultured Picovirinae virus assembled from ERR7738555. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538521 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 19.6256 MAG coverage software Reads (ERR7738555) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567620) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_3536_length_15071_cov_10.973389 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_3536_length_15071_cov_10.973389 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098563 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia sp900552665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745366_virus.2096 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae; Picovirinae virus enrichment approach none ERS11140491 SAMEA13538522 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738555. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538522 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 46.9801 MAG coverage software Reads (ERR7738555) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567620) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_653_length_61832_cov_27.487653 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6888888888888889 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_653_length_61832_cov_27.487653 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738555_virus.653 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140492 SAMEA13538523 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738555. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538523 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 8.48941 MAG coverage software Reads (ERR7738555) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567620) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 232 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_984_length_45975_cov_4.744586 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; HMM-based (lower-bound) completeness score 79.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_24_2346__NODE_984_length_45975_cov_4.744586 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738555_virus.984 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140493 SAMEA13538524 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738556. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538524 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 19.2109 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_163_length_161575_cov_11.108905_1 Viral contig found in MAG ERR7738556_bin.158 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8205128205128205 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_163_length_161575_cov_11.108905_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.329 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__UBA1191 sp900549125 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.2635 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140494 SAMEA13538525 2133760 Siphoviridae environmental samples This sample represents an uncultured Cellulophaga phage Ingeline_8 provirus assembled from ERR7738556. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538525 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 69.0428 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 53 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_286_length_129291_cov_43.593697_1 Viral contig found in MAG ERR7738556_bin.151 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_286_length_129291_cov_43.593697_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cellulophaga phage Ingeline_8 virus enrichment approach none ERS11140495 SAMEA13538526 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738556. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538526 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 9.32291 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 97 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_601_length_84712_cov_5.173226_1 Viral contig found in MAG ERR7738556_bin.303 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_601_length_84712_cov_5.173226_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.1513 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140496 SAMEA13538527 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738556. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538527 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 28.2616 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_119_length_186900_cov_16.453381 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.7183098591549296 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_119_length_186900_cov_16.453381 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140497 SAMEA13538528 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538528 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:16Z INSDC last update 2022-12-27T19:09:16Z INSDC status public MAG coverage depth 21.8832 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1406_length_49144_cov_13.090529 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; ITR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8780487804878049 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1406_length_49144_cov_13.090529 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738273_bin.125 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__WG-1;s__WG-1 sp900539665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.1406 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140498 SAMEA13538529 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738556. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538529 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 15.5117 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 601 Number of CRISPR spacer hits supporting host taxonomy 1248 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1579_length_45579_cov_8.851875 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5576923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1579_length_45579_cov_8.851875 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11140499 SAMEA13538530 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538530 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 19.2911 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 167 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1681_length_43729_cov_10.992532 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6764705882352942 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1681_length_43729_cov_10.992532 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.1681 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140500 SAMEA13538531 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538531 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 11.9848 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1873_length_40551_cov_6.864679 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_1873_length_40551_cov_6.864679 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.1873 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140501 SAMEA13538532 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538532 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 15.2877 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 70 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_2118_length_37099_cov_8.689509 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_2118_length_37099_cov_8.689509 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.2118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140502 SAMEA13538533 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.03945538818076477 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538533 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 32.7425 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 94 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_2466_length_33223_cov_19.315815 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_2466_length_33223_cov_19.315815 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.1150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140503 SAMEA13538534 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538534 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 13.3656 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_2773_length_30500_cov_7.821714 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_2773_length_30500_cov_7.821714 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746741_bin.80 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;s__RUG572 sp900547945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.1666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140504 SAMEA13538535 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738556. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538535 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:13Z INSDC last update 2022-12-27T00:30:13Z INSDC status public MAG coverage depth 386.77 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_315_length_121941_cov_217.359934 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.943661971830986 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_315_length_121941_cov_217.359934 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738531_virus.150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140505 SAMEA13538536 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu virus assembled from ERR7738556. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538536 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 11.8022 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 183 Number of CRISPR spacer hits supporting host taxonomy 296 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_3822_length_23822_cov_6.814108 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_3822_length_23822_cov_6.814108 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.698 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11140506 SAMEA13538537 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538537 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 18.9518 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_459_length_97580_cov_11.001579 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2692307692307692 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_459_length_97580_cov_11.001579 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747782_bin.13 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola sp000434735 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.459 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140507 SAMEA13538538 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738556. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538538 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 80.4909 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_5578_length_17645_cov_45.777892 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_5578_length_17645_cov_45.777892 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.7124 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140508 SAMEA13538539 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738556. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538539 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 42.7998 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_7067_length_14532_cov_24.126116 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_7067_length_14532_cov_24.126116 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.7067 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11140509 SAMEA13538540 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738556. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538540 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 31.448 MAG coverage software Reads (ERR7738556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560131) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_P_3_2141__NODE_9931_length_11157_cov_18.286101 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586127 sample name Hadza_MoBio_hadza-E-H_P_3_2141__NODE_9931_length_11157_cov_18.286101 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738513_bin.13 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900551275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0055675 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11140510 SAMEA13538541 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738557. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538541 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 14.1827 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1277_length_58633_cov_8.375640_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1277_length_58633_cov_8.375640_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_provirus.1277 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140511 SAMEA13538542 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738557. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538542 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 17.8768 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2387_length_39914_cov_10.660115_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2387_length_39914_cov_10.660115_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.33 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448;s__CAG-448 sp003150135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_provirus.2387 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140513 SAMEA13538544 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738557. BACPHLIP temperate score 0.05422945491458051 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538544 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 8.81792 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1131_length_62865_cov_5.193126 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1131_length_62865_cov_5.193126 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.1131 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140514 SAMEA13538545 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538545 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 17.2189 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1352_length_56811_cov_10.323563 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9696969696969696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1352_length_56811_cov_10.323563 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.224 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__Ruminococcus sp900540005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.840 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140515 SAMEA13538546 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 0.11513032049760293 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538546 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 33.7359 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1547_length_53013_cov_20.186659 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1547_length_53013_cov_20.186659 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME155972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D;s__Haemophilus_D parainfluenzae_K vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.1545 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140516 SAMEA13538547 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538547 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 10.7316 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1819_length_48024_cov_6.372328 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_1819_length_48024_cov_6.372328 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME285832 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002300055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.1819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140517 SAMEA13538548 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538548 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 66.0656 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2074_length_44224_cov_39.810248 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2074_length_44224_cov_39.810248 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.2074 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140518 SAMEA13538549 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538549 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 15.1051 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2268_length_41288_cov_9.141055 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2268_length_41288_cov_9.141055 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745963_bin.383 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745743_virus.1484 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140519 SAMEA13538550 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738557. BACPHLIP temperate score 0.12230176211453749 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538550 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 12.3081 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2467_length_38998_cov_7.286118 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2467_length_38998_cov_7.286118 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738141_virus.285 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140520 SAMEA13538551 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538551 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 143.18 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2598_length_37584_cov_84.829125 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_2598_length_37584_cov_84.829125 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME011266 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696;s__UMGS1696 sp900554225 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.2598 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140521 SAMEA13538552 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738557. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538552 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 32.8612 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_288_length_123276_cov_20.122947 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5217391304347826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_288_length_123276_cov_20.122947 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.288 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140522 SAMEA13538553 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738557. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538553 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 8.25287 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_32684_length_5374_cov_4.895412 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_32684_length_5374_cov_4.895412 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME040022 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA1409;s__UBA1409 sp002338885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.32684 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140523 SAMEA13538554 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538554 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 12.6206 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_3827_length_29062_cov_7.421080 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3636363636363637 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_3827_length_29062_cov_7.421080 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1564 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140524 SAMEA13538555 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738557. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538555 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:15Z INSDC last update 2022-12-27T19:09:15Z INSDC status public MAG coverage depth 13.8467 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_431_length_101980_cov_8.276420 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5822784810126582 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_431_length_101980_cov_8.276420 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0370433 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140525 SAMEA13538556 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 0.13997797356828195 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538556 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 20.9663 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_4664_length_25383_cov_13.297044 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_4664_length_25383_cov_13.297044 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.4664 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140526 SAMEA13538557 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738557. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538557 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 8.29262 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_6136_length_20603_cov_4.803274 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_6136_length_20603_cov_4.803274 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746285_bin.102 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFTH01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_provirus.3166142 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140527 SAMEA13538558 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738557. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538558 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 8.59923 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_8768_length_15785_cov_5.042271 Viral contig found in MAG ERR7738557_bin.268 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_8768_length_15785_cov_5.042271 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738584_bin.295 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-460;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0129178 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140528 SAMEA13538559 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738558. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538559 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 9.84947 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 244 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1336_length_47482_cov_5.608396_1 Viral contig found in MAG ERR7738558_bin.164 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5862068965517241 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1336_length_47482_cov_5.608396_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_provirus.1336 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140529 SAMEA13538560 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7738558. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538560 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 25.8017 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_392_length_91868_cov_14.892430_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6060606060606061 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_392_length_91868_cov_14.892430_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_provirus.392 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11140530 SAMEA13538561 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738558. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538561 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 15.0954 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_856_length_62062_cov_8.772542_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_856_length_62062_cov_8.772542_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738575_provirus.18 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140531 SAMEA13538562 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738558. BACPHLIP temperate score 0.3625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538562 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 186.44 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1285_length_48724_cov_107.346065 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1285_length_48724_cov_107.346065 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_provirus.57 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140532 SAMEA13538563 2100421 uncultured Caudovirales phage This sample represents an uncultured Vectrevirus virus assembled from ERR7738558. BACPHLIP temperate score 0.03964755271026948 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538563 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 9.32471 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1480_length_44217_cov_5.173108 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1480_length_44217_cov_5.173108 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.1480 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae; Molineuxvirinae; Vectrevirus virus enrichment approach none ERS11140533 SAMEA13538564 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738558. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538564 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 16.6045 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 113 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1689_length_40662_cov_10.553604 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_1689_length_40662_cov_10.553604 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.1689 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140534 SAMEA13538565 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738558. BACPHLIP temperate score 0.03727973568281938 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538565 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 23.173 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_191_length_124683_cov_13.341147 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8043478260869565 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_191_length_124683_cov_13.341147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.191 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140535 SAMEA13538566 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738558. BACPHLIP temperate score 0.6129947229551451 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538566 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 62.5638 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_2051_length_35424_cov_39.039551 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_2051_length_35424_cov_39.039551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.754 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140536 SAMEA13538567 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus virus assembled from ERR7738558. BACPHLIP temperate score 0.29000921161364956 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538567 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 9.4344 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3255 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_2654_length_29342_cov_5.313617 Viral contig found in MAG ERR7738558_bin.51 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8809523809523809 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_2654_length_29342_cov_5.313617 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0228353 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11140537 SAMEA13538568 336724 Myoviridae environmental samples This sample represents an uncultured Yongloolinvirus virus assembled from ERR7738558. BACPHLIP temperate score 0.01734581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13538568 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-28T19:46:11Z INSDC status public MAG coverage depth 25.9949 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 73 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_3474_length_23421_cov_14.892606 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_3474_length_23421_cov_14.892606 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0289566 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Yongloolinvirus virus enrichment approach none ERS11140538 SAMEA13538569 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738558. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538569 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 15.7732 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_4240_length_19890_cov_9.115040 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_4240_length_19890_cov_9.115040 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.4240 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140539 SAMEA13538570 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738558. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538570 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 48.9243 MAG coverage software Reads (ERR7738558) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567246) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_839_length_62992_cov_28.187745 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787343 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_13_CHE0014TZ__NODE_839_length_62992_cov_28.187745 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.839 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140540 SAMEA13538571 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738559. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538571 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:18Z INSDC last update 2022-12-27T00:30:18Z INSDC status public MAG coverage depth 32.6275 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1156_length_52605_cov_19.367975_1 Viral contig found in MAG ERR7738559_bin.162 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1156_length_52605_cov_19.367975_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_provirus.1156 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140541 SAMEA13538572 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738559. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538572 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 14.5909 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 119 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1484_length_44674_cov_8.964168_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9032258064516128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1484_length_44674_cov_8.964168_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_virus.2710 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140542 SAMEA13538573 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738559. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538573 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 23.1116 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1766_length_40357_cov_15.442602_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1766_length_40357_cov_15.442602_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_provirus.1766 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140543 SAMEA13538574 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738559. BACPHLIP temperate score 0.11996874984972046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538574 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 34.1137 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_3375_length_25726_cov_22.219814_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_3375_length_25726_cov_22.219814_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME104932 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I;s__Eubacterium_I ramulus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.2244 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140544 SAMEA13538575 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738559. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538575 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 14.4268 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 213 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_563_length_77539_cov_8.758423_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_563_length_77539_cov_8.758423_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0375088 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140545 SAMEA13538576 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538576 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 14.7049 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1051_length_55831_cov_8.741543 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1051_length_55831_cov_8.741543 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738159_bin.38 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales_A;f__UBA1381;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.595 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140546 SAMEA13538577 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538577 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 11.8789 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1510_length_44136_cov_7.040219 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1510_length_44136_cov_7.040219 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_virus.1510 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140547 SAMEA13538578 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538578 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 19.1236 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1811_length_39699_cov_12.397254 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_1811_length_39699_cov_12.397254 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140265 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia;s__Blautia stercoris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_virus.1811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140548 SAMEA13538579 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538579 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 8.25873 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_2145_length_35735_cov_4.813029 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_2145_length_35735_cov_4.813029 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_virus.2145 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140549 SAMEA13538580 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538580 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 28.5095 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_2804_length_29627_cov_17.852386 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_2804_length_29627_cov_17.852386 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_provirus.1734 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140550 SAMEA13538581 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 0.11545151506649157 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538581 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 10.0421 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 148 Number of CRISPR spacer hits supporting host taxonomy 421 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_3346_length_25961_cov_5.857016 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_3346_length_25961_cov_5.857016 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME216999 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales_A;f__UBA1381;g__CAG-41;s__CAG-41 sp900066215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_virus.3346 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140551 SAMEA13538582 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538582 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 103.129 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_4395_length_20795_cov_63.404817 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_4395_length_20795_cov_63.404817 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_virus.4395 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140552 SAMEA13538583 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738559. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538583 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 19.1059 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_5016_length_18660_cov_11.818490 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_5016_length_18660_cov_11.818490 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.4536 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140553 SAMEA13538584 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538584 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 23.9751 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_7734_length_13249_cov_15.160112 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_7734_length_13249_cov_15.160112 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.10211 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140554 SAMEA13538585 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738559. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538585 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 14.8335 MAG coverage software Reads (ERR7738559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567799) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 547 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_950_length_59280_cov_8.880361 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585783 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_8_1528__NODE_950_length_59280_cov_8.880361 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.540 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140555 SAMEA13538586 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738560. BACPHLIP temperate score 0.877477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538586 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 8.19167 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_2532_length_26534_cov_3.997203_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_2532_length_26534_cov_3.997203_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140556 SAMEA13538587 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7738560. BACPHLIP temperate score 0.01554291393558823 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538587 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 19.8896 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_69_length_233941_cov_10.983760_1 Viral contig found in MAG ERR7738560_bin.207 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5277777777777778 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_69_length_233941_cov_10.983760_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_provirus.69 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11140557 SAMEA13538588 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738560. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538588 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 37.14 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1059_length_51736_cov_20.718055 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1059_length_51736_cov_20.718055 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.1059 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140558 SAMEA13538589 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738560. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538589 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 88.627 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 672 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1359_length_42887_cov_48.104952 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.65625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1359_length_42887_cov_48.104952 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.1359 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11140559 SAMEA13538590 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738560. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538590 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 16.9399 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 174 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1498_length_39594_cov_8.988790 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1498_length_39594_cov_8.988790 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.1498 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140560 SAMEA13538591 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738560. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538591 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 8.95811 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 115 Number of CRISPR spacer hits supporting host taxonomy 227 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1600_length_37625_cov_4.486284 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1600_length_37625_cov_4.486284 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140561 SAMEA13538592 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738560. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538592 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 21.4209 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1749_length_35323_cov_11.608750 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_1749_length_35323_cov_11.608750 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME256624 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-272;s__CAG-272 sp000433515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.1896 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140562 SAMEA13538593 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738560. BACPHLIP temperate score 0.01445538818076477 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538593 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 9.04106 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_2216_length_29401_cov_4.476163 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_2216_length_29401_cov_4.476163 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746757_bin.199 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436;s__UBA1436 sp900541355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738271_provirus.247 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140563 SAMEA13538594 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738560. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538594 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 10.1878 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_3323_length_21477_cov_5.180981 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_3323_length_21477_cov_5.180981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.3323 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140564 SAMEA13538595 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738560. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538595 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 25.2706 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_426_length_93931_cov_27.872685 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.543859649122807 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_426_length_93931_cov_27.872685 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.426 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140565 SAMEA13538596 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738560. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538596 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 71.2161 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 231 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_697_length_68793_cov_39.774128 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_697_length_68793_cov_39.774128 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.697 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140566 SAMEA13538597 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738560. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538597 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 66.2694 MAG coverage software Reads (ERR7738560) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567601) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_988_length_54475_cov_36.689069 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787413 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_9_THA1076JZ__NODE_988_length_54475_cov_36.689069 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.1040 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140567 SAMEA13538598 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738561. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538598 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 16.1185 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1611_length_33737_cov_9.810131_1 Viral contig found in MAG ERR7738561_bin.248 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1611_length_33737_cov_9.810131_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746785_bin.294 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.1004 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140568 SAMEA13538599 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738561. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538599 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 16.2195 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_433_length_74447_cov_9.940715_1 Viral contig found in MAG ERR7738561_bin.157 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_433_length_74447_cov_9.940715_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_provirus.433 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140569 SAMEA13538600 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738561. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538600 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 26.7037 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_774_length_53272_cov_16.516421_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_774_length_53272_cov_16.516421_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738660_provirus.1174 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140570 SAMEA13538601 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738561. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538601 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 51.3716 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_102_length_152677_cov_31.784168 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 19 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.6981132075471698 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_102_length_152677_cov_31.784168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001115 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_E vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.214 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140571 SAMEA13538602 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738561. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538602 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 8.54912 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1225_length_39974_cov_5.360403 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8214285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1225_length_39974_cov_5.360403 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_virus.1225 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140572 SAMEA13538603 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738561. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538603 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 20.7783 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 410 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1400_length_36960_cov_12.586747 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1400_length_36960_cov_12.586747 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1565 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140573 SAMEA13538604 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738561. BACPHLIP temperate score 0.5895374449339206 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538604 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:22Z INSDC last update 2022-12-27T00:30:22Z INSDC status public MAG coverage depth 46.0376 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1596_length_33855_cov_27.343271 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_1596_length_33855_cov_27.343271 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.1676 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140574 SAMEA13538605 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7738561. BACPHLIP temperate score 0.17779457421297337 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538605 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 25.4954 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 673 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_2070_length_28804_cov_15.409963 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8055555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_2070_length_28804_cov_15.409963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_provirus.787 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11140575 SAMEA13538606 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738561. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538606 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 11.8892 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 114 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_2603_length_24718_cov_7.199424 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_2603_length_24718_cov_7.199424 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738660_virus.4711 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140576 SAMEA13538607 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738561. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538607 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 10.6103 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_306_length_88880_cov_6.428477 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6739130434782609 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_306_length_88880_cov_6.428477 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745854_bin.309 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738228_virus.41 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140577 SAMEA13538608 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738561. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538608 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 10.388 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_3850_length_19052_cov_6.052964 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; HMM-based (lower-bound) completeness score 58.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_3850_length_19052_cov_6.052964 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.8397 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140578 SAMEA13538609 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738561. BACPHLIP temperate score 0.17514496130346496 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538609 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 14.1296 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_4485_length_17171_cov_8.495905 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_4485_length_17171_cov_8.495905 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_virus.4485 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140579 SAMEA13538610 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738561. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538610 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 13.712 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 1120 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_629_length_60127_cov_8.192939 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_629_length_60127_cov_8.192939 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140580 SAMEA13538611 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738561. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538611 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 13.6325 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 253 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_732_length_55297_cov_8.175317 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_732_length_55297_cov_8.175317 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737953_virus.234 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140581 SAMEA13538612 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738561. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538612 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 5.76285 MAG coverage software Reads (ERR7738561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567869) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_9640_length_9798_cov_3.270034 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585818 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_16_1564__NODE_9640_length_9798_cov_3.270034 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738150_virus.4712 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11140582 SAMEA13538613 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738562. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538613 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 21.1855 MAG coverage software Reads (ERR7738562) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Pilot_MoBio_Fiber_G_23_1002__NODE_1791_length_35634_cov_12.355992_1 Viral contig found in MAG ERR7738562_bin.27 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384124 sample name Pilot_MoBio_Fiber_G_23_1002__NODE_1791_length_35634_cov_12.355992_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0251367 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140583 SAMEA13538614 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738562. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538614 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 11.7866 MAG coverage software Reads (ERR7738562) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 92 Number of CRISPR spacer hits supporting host taxonomy 134 Submitter Id Pilot_MoBio_Fiber_G_23_1002__NODE_278_length_125362_cov_6.853598_1 Viral contig found in MAG ERR7738562_bin.17 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384124 sample name Pilot_MoBio_Fiber_G_23_1002__NODE_278_length_125362_cov_6.853598_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0327705 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140584 SAMEA13538615 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738562. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538615 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 22.1035 MAG coverage software Reads (ERR7738562) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 65 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Pilot_MoBio_Fiber_G_23_1002__NODE_903_length_64989_cov_12.691074_1 Viral contig found in MAG ERR7738562_bin.100 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384124 sample name Pilot_MoBio_Fiber_G_23_1002__NODE_903_length_64989_cov_12.691074_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738562_provirus.903 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140585 SAMEA13538616 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738562. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538616 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 789.882 MAG coverage software Reads (ERR7738562) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 412 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Pilot_MoBio_Fiber_G_23_1002__NODE_1327_length_47118_cov_461.921792 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384124 sample name Pilot_MoBio_Fiber_G_23_1002__NODE_1327_length_47118_cov_461.921792 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0377017 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140586 SAMEA13538617 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738562. BACPHLIP temperate score 0.01542166484257643 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538617 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 16.0123 MAG coverage software Reads (ERR7738562) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 166 Submitter Id Pilot_MoBio_Fiber_G_23_1002__NODE_1845_length_34522_cov_9.385281 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384124 sample name Pilot_MoBio_Fiber_G_23_1002__NODE_1845_length_34522_cov_9.385281 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__Bilophila wadsworthia vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738562_virus.1845 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140587 SAMEA13538618 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738562. BACPHLIP temperate score 0.1885875257548235 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538618 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 7.45285 MAG coverage software Reads (ERR7738562) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 406 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Pilot_MoBio_Fiber_G_23_1002__NODE_2728_length_23164_cov_4.115346 Viral contig found in MAG ERR7738562_bin.1 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384124 sample name Pilot_MoBio_Fiber_G_23_1002__NODE_2728_length_23164_cov_4.115346 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000511 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides fragilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738937_provirus.68_2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140588 SAMEA13538619 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738563. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538619 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 234.687 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_11_length_383712_cov_133.232213_1 Viral contig found in MAG ERR7738563_bin.204 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_11_length_383712_cov_133.232213_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_provirus.11 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140589 SAMEA13538620 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738563. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538620 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 19.2484 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1906_length_34522_cov_11.178168_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1906_length_34522_cov_11.178168_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_provirus.1906 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140590 SAMEA13538621 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738563. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538621 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 23.5486 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_550_length_74665_cov_13.422467_1 Viral contig found in MAG ERR7738563_bin.47 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_550_length_74665_cov_13.422467_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_provirus.550 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140591 SAMEA13538622 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738563. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538622 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 58.4705 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1066_length_50295_cov_35.974909 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1066_length_50295_cov_35.974909 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.671 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140592 SAMEA13538623 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738563. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538623 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 47.9432 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_12663_length_8198_cov_28.967738 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_12663_length_8198_cov_28.967738 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.12663 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11140593 SAMEA13538624 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538624 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 26.4992 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 97 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1467_length_41242_cov_15.315559 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1467_length_41242_cov_15.315559 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.1467 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140594 SAMEA13538625 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538625 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 72.8552 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1594_length_38762_cov_41.073930 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1594_length_38762_cov_41.073930 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.1594 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140595 SAMEA13538626 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538626 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 17.1149 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1730_length_36742_cov_9.696277 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_1730_length_36742_cov_9.696277 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.3571503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140596 SAMEA13538627 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538627 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 12.419 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_2008_length_33177_cov_6.811450 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_2008_length_33177_cov_6.811450 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.2008 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140597 SAMEA13538628 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538628 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 14.8796 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_2346_length_29948_cov_8.821365 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 70 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_2346_length_29948_cov_8.821365 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.2346 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140598 SAMEA13538629 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538629 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 28.9962 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 213 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_286_length_106819_cov_16.498642 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_286_length_106819_cov_16.498642 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140599 SAMEA13538630 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538630 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 247.659 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 464 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_324_length_100135_cov_140.692478 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.35 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_324_length_100135_cov_140.692478 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140600 SAMEA13538631 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538631 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 23.9527 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_3964_length_20505_cov_14.076757 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_3964_length_20505_cov_14.076757 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.3964 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140601 SAMEA13538632 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538632 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 92.1263 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_5120_length_16755_cov_53.547368 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; ITR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_5120_length_16755_cov_53.547368 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.5120 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140602 SAMEA13538633 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738563. BACPHLIP temperate score 0.26998632496778685 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538633 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 31.8569 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_65_length_188306_cov_17.959682 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.5636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_65_length_188306_cov_17.959682 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.65 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140603 SAMEA13538634 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538634 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 95.3606 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_771_length_61345_cov_54.181188 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9142857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_771_length_61345_cov_54.181188 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018425 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__CAG-791 sp000431495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738536_provirus.683 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140604 SAMEA13538635 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738563. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538635 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 247.164 MAG coverage software Reads (ERR7738563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560756) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_G_1_1731__NODE_922_length_55580_cov_138.828334 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585974 sample name Hadza_MoBio_hadza-E-H_G_1_1731__NODE_922_length_55580_cov_138.828334 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_virus.922 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140605 SAMEA13538636 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738564. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538636 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 19.0925 MAG coverage software Reads (ERR7738564) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567396) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_3_THA0078JZ__NODE_25_length_280696_cov_10.979659_1_1 Viral contig found in MAG ERR7738564_bin.35 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.8444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787400 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_3_THA0078JZ__NODE_25_length_280696_cov_10.979659_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738564_provirus.25 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140606 SAMEA13538637 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738564. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538637 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 218.891 MAG coverage software Reads (ERR7738564) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567396) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 108 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_3_THA0078JZ__NODE_580_length_46053_cov_127.457608_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787400 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_3_THA0078JZ__NODE_580_length_46053_cov_127.457608_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738144_virus.294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140607 SAMEA13538638 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738564. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538638 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 131.394 MAG coverage software Reads (ERR7738564) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567396) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 98 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_3_THA0078JZ__NODE_150_length_126186_cov_76.725135 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787400 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_3_THA0078JZ__NODE_150_length_126186_cov_76.725135 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738564_virus.150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140608 SAMEA13538639 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738565. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538639 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 8.96124 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_1147_length_53661_cov_5.252034_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_1147_length_53661_cov_5.252034_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.2186 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140609 SAMEA13538640 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738565. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538640 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 52.5479 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_243_length_128332_cov_31.715824_1 Viral contig found in MAG ERR7738565_bin.244 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9117647058823528 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_243_length_128332_cov_31.715824_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.2420 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140610 SAMEA13538641 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738565. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538641 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 24.9685 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_553_length_83843_cov_14.822637_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_553_length_83843_cov_14.822637_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738531_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_B;c__Peptococcia;o__Peptococcales;f__Peptococcaceae;g__UMGS1590;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_provirus.931 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140611 SAMEA13538642 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738565. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538642 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 27.5293 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 214 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_93_length_190118_cov_16.501355_1 Viral contig found in MAG ERR7738565_bin.198 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_93_length_190118_cov_16.501355_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.2062 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140612 SAMEA13538643 2133760 Siphoviridae environmental samples This sample represents an uncultured Vegasvirus virus assembled from ERR7738565. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538643 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 18.766 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_1449_length_45993_cov_11.296346 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_1449_length_45993_cov_11.296346 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_virus.1449 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Gochnauervirinae; Vegasvirus virus enrichment approach none ERS11140613 SAMEA13538644 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738565. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538644 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 18.7159 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 114 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_1739_length_41278_cov_11.333536 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_1739_length_41278_cov_11.333536 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_virus.1739 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140614 SAMEA13538645 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738565. BACPHLIP temperate score 0.18491189427312776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538645 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 9.83415 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_2068_length_36815_cov_5.660025 Viral contig found in MAG ERR7738565_bin.257 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9666666666666668 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_2068_length_36815_cov_5.660025 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_virus.1263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140615 SAMEA13538646 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738565. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538646 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 17.0867 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 67 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_2306_length_34238_cov_10.340213 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_2306_length_34238_cov_10.340213 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_virus.2306 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140616 SAMEA13538647 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738565. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538647 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 492.588 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_3021_length_28410_cov_298.815268 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_3021_length_28410_cov_298.815268 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746440_virus.1641 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140617 SAMEA13538648 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738565. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538648 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 43.3311 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_3879_length_24054_cov_26.643492 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_3879_length_24054_cov_26.643492 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.2314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140619 SAMEA13538650 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738565. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538650 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 8.85478 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_6235_length_17317_cov_5.437877 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_6235_length_17317_cov_5.437877 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.6263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140620 SAMEA13538651 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738565. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538651 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 7.02077 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_9052_length_13197_cov_3.861890 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_9052_length_13197_cov_3.861890 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142391 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P perfringens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_virus.9052 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140621 SAMEA13538652 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738566. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538652 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 20.9989 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1691_length_41006_cov_11.866305_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1691_length_41006_cov_11.866305_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_virus.1419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140622 SAMEA13538653 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738566. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538653 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 63.9307 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 209 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_275_length_111215_cov_39.308418_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_275_length_111215_cov_39.308418_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_provirus.117 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140623 SAMEA13538654 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738566. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538654 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 14.6831 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_7_length_422537_cov_8.095491_1 Viral contig found in MAG ERR7738566_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_7_length_422537_cov_8.095491_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746111_bin.94 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_provirus.7 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140624 SAMEA13538655 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738566. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538655 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 40.9675 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 94 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_962_length_58891_cov_24.167375_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_962_length_58891_cov_24.167375_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.1765 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140625 SAMEA13538656 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738566. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538656 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 34.6545 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1286_length_48769_cov_19.119773 Viral contig found in MAG ERR7738566_bin.260 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1286_length_48769_cov_19.119773 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.1286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140627 SAMEA13538658 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738566. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538658 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 16.7888 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_16057_length_6690_cov_11.712990 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_16057_length_6690_cov_11.712990 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.16057 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140628 SAMEA13538659 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738566. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538659 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 34.0454 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 143 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1781_length_39478_cov_18.570899 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1781_length_39478_cov_18.570899 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.1781 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140629 SAMEA13538660 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738566. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538660 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 40.5124 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 110 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_2096_length_35351_cov_23.947724 Viral contig found in MAG ERR7738566_bin.193 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_2096_length_35351_cov_23.947724 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0336364 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140630 SAMEA13538661 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738566. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538661 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 32.3137 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 69 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_2997_length_27116_cov_17.803358 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_2997_length_27116_cov_17.803358 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_provirus.18 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140631 SAMEA13538662 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738566. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538662 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 150.433 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_3400_length_24475_cov_82.934216 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_3400_length_24475_cov_82.934216 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME023798 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900543155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.242 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140633 SAMEA13538664 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738566. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538664 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 12.6707 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_7250_length_13056_cov_6.927892 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_7250_length_13056_cov_6.927892 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.139 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.7250 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140634 SAMEA13538665 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738566. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538665 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 26.9975 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 146 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_933_length_60004_cov_15.117276 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.40816326530612246 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_933_length_60004_cov_15.117276 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140635 SAMEA13538666 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738567. BACPHLIP temperate score 0.08134553233439058 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538666 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 13.0597 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1629_length_48601_cov_7.400235_1 Viral contig found in MAG ERR7738567_bin.167 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1629_length_48601_cov_7.400235_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_provirus.2113 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140636 SAMEA13538667 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738567. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538667 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 30.1242 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_259_length_138001_cov_18.425705_1 Viral contig found in MAG ERR7738567_bin.318 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; HMM-based (lower-bound) completeness score 52.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_259_length_138001_cov_18.425705_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_provirus.259 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140637 SAMEA13538669 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738567. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538669 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 123.291 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 309 Number of CRISPR spacer hits supporting host taxonomy 794 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_923_length_69203_cov_71.831033_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_923_length_69203_cov_71.831033_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_provirus.923 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140638 SAMEA13538670 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738567. BACPHLIP temperate score 0.575 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538670 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 20.3508 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1339_length_54863_cov_11.482696 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1339_length_54863_cov_11.482696 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738604_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432655 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.1001 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140639 SAMEA13538671 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738567. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538671 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 22.6315 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 249 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1644_length_48354_cov_12.916813 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9696969696969696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1644_length_48354_cov_12.916813 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372952 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11140640 SAMEA13538672 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738567. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538672 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 335.35 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1989_length_42583_cov_189.416412 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9310344827586208 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_1989_length_42583_cov_189.416412 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257123 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900547315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.1989 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140642 SAMEA13538674 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738567. BACPHLIP temperate score 0.1682162390555499 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538674 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 20.1964 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_2617_length_35490_cov_11.811764 Viral contig found in MAG ERR7738567_bin.291 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_2617_length_35490_cov_11.811764 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738257_provirus.416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140643 SAMEA13538675 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738567. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538675 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 13.12 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 81 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_3065_length_31521_cov_7.410444 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_3065_length_31521_cov_7.410444 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.2306 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140644 SAMEA13538676 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738567. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538676 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 11.946 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_3454_length_28641_cov_6.744819 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_3454_length_28641_cov_6.744819 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.3454 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140645 SAMEA13538677 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738567. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538677 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 13.011 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 91 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_4494_length_23170_cov_6.997012 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_4494_length_23170_cov_6.997012 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140646 SAMEA13538678 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus virus assembled from ERR7738567. BACPHLIP temperate score 0.16913360473183253 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538678 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 17.6234 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_5327_length_20055_cov_10.034938 Viral contig found in MAG ERR7738567_bin.167 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_5327_length_20055_cov_10.034938 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252578 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.5327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11140648 SAMEA13538680 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738568. BACPHLIP temperate score 0.375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538680 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 11.5608 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_140_length_173287_cov_6.905427_1 Viral contig found in MAG ERR7738568_bin.86 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_140_length_173287_cov_6.905427_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738537_provirus.867 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140649 SAMEA13538681 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738568. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538681 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 18.3709 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2513_length_36415_cov_10.838158_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2513_length_36415_cov_10.838158_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738233_virus.443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140650 SAMEA13538682 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738568. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538682 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 32.0657 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_614_length_86453_cov_19.956261_1 Viral contig found in MAG ERR7738568_bin.326 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5277777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_614_length_86453_cov_19.956261_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738568_bin.326 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__SFEL01;s__SFEL01 sp004557245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_provirus.614 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140651 SAMEA13538683 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538683 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 19.4978 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_1142_length_60584_cov_11.899929 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_1142_length_60584_cov_11.899929 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738566_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140652 SAMEA13538684 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538684 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 43.045 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_1331_length_55331_cov_25.507601 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9705882352941176 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_1331_length_55331_cov_25.507601 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000448 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900066885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.741 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140653 SAMEA13538685 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538685 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 14.4617 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 209 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_1699_length_47494_cov_8.518548 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8387096774193549 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_1699_length_47494_cov_8.518548 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_virus.1699 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140655 SAMEA13538687 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538687 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 10.0035 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 129 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2243_length_39252_cov_5.850645 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2243_length_39252_cov_5.850645 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME246707 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__Phil1;s__Phil1 sp001940855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_virus.2243 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140656 SAMEA13538688 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538688 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 20.1463 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 114 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2416_length_37520_cov_12.074406 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2416_length_37520_cov_12.074406 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738241_virus.1296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140657 SAMEA13538689 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538689 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 13.855 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2760_length_34182_cov_8.616215 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.45 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2760_length_34182_cov_8.616215 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_virus.2315 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140658 SAMEA13538690 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.08458149779735687 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538690 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 10.5154 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_3455_length_28959_cov_6.195070 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_3455_length_28959_cov_6.195070 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738213_virus.1405 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140659 SAMEA13538691 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538691 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 6.36559 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_5340_length_20525_cov_3.508852 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_5340_length_20525_cov_3.508852 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.1610 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140661 SAMEA13538693 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738569. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538693 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 34.0328 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_174_length_110213_cov_20.776976_1 Viral contig found in MAG ERR7738569_bin.160 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_174_length_110213_cov_20.776976_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.2010 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140662 SAMEA13538694 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738569. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538694 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 28.0095 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 53 Number of CRISPR spacer hits supporting host taxonomy 1082 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_537_length_67752_cov_16.991090_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_537_length_67752_cov_16.991090_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738221_virus.272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140663 SAMEA13538695 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738569. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538695 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 400.375 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2031 Number of CRISPR spacer hits supporting host taxonomy 584 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_935_length_49953_cov_251.107827_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_935_length_49953_cov_251.107827_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140664 SAMEA13538696 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738569. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538696 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 23.8746 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 985 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_1342_length_41028_cov_16.542819 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_1342_length_41028_cov_16.542819 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_provirus.343 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140665 SAMEA13538697 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738569. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538697 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 38.2577 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_1563_length_37773_cov_22.701772 Viral contig found in MAG ERR7738569_bin.152 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_1563_length_37773_cov_22.701772 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_virus.1326 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140666 SAMEA13538698 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738569. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538698 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 17.4648 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_193_length_106570_cov_10.271849 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_193_length_106570_cov_10.271849 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738569_virus.193 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140667 SAMEA13538699 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738569. BACPHLIP temperate score 0.00991189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538699 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 33.5066 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_228_length_98051_cov_19.737216 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.922077922077922 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_228_length_98051_cov_19.737216 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11140668 SAMEA13538700 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738569. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538700 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 7.74486 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_27133_length_5253_cov_4.670015 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_27133_length_5253_cov_4.670015 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738588_bin.321 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger sp004555405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_virus.17872 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140670 SAMEA13538702 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738569. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538702 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 11.8698 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_4072_length_21018_cov_6.878898 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_4072_length_21018_cov_6.878898 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745854_bin.180 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_provirus.219 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140671 SAMEA13538703 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738569. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538703 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 24.8132 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_620_length_61822_cov_14.701450 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48484848484848486 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_620_length_61822_cov_14.701450 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738569_virus.620 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140672 SAMEA13538704 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7738569. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538704 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 23.2661 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 178 Number of CRISPR spacer hits supporting host taxonomy 1185 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_850_length_52883_cov_13.903893 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_850_length_52883_cov_13.903893 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0328330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11140673 SAMEA13538705 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738570. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538705 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 71.4158 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_120_length_198478_cov_40.655072_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5151515151515151 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_120_length_198478_cov_40.655072_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.44 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140674 SAMEA13538706 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738570. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538706 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 13.0353 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_192_length_162322_cov_7.447385_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_192_length_162322_cov_7.447385_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__UMGS124;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_provirus.192 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140676 SAMEA13538708 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738570. BACPHLIP temperate score 0.889977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538708 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 30.3573 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_512_length_100202_cov_17.159660_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_512_length_100202_cov_17.159660_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_provirus.512 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140677 SAMEA13538709 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738570. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538709 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 39.1499 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_9_length_458744_cov_22.631277_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.5588235294117647 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_9_length_458744_cov_22.631277_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140678 SAMEA13538710 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738570. BACPHLIP temperate score 0.11996874984972046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538710 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 52.4646 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_11112_length_11900_cov_29.818236 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; ITR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_11112_length_11900_cov_29.818236 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.11112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11140679 SAMEA13538711 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738570. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538711 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 44.8982 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 339 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_1411_length_54617_cov_25.954474 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9577464788732394 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_1411_length_54617_cov_25.954474 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.2014 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140680 SAMEA13538712 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738570. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538712 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 18.7089 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 304 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_1926_length_44271_cov_10.824931 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7714285714285715 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_1926_length_44271_cov_10.824931 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140681 SAMEA13538713 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738570. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538713 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 11.9674 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_2296_length_39061_cov_6.826031 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_2296_length_39061_cov_6.826031 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_virus.748 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140682 SAMEA13538714 340016 uncultured virus This sample represents an uncultured Pseudomonas phage PPAT virus assembled from ERR7738570. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538714 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 21.3239 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_2680_length_35160_cov_12.142890 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_2680_length_35160_cov_12.142890 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.2680 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Pseudomonas phage PPAT virus enrichment approach none ERS11140684 SAMEA13538716 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738570. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538716 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 10.4487 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_3844_length_27448_cov_5.846918 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_3844_length_27448_cov_5.846918 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME138453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus;s__Lactococcus lactis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.3844 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140685 SAMEA13538717 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738570. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538717 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 686.24 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_501_length_101384_cov_388.881242 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_501_length_101384_cov_388.881242 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.457 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140686 SAMEA13538718 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738570. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538718 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 11.1922 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_583_length_93202_cov_6.299329 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_583_length_93202_cov_6.299329 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738651_bin.237 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA5905;s__UBA5905 sp900763035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140687 SAMEA13538719 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738570. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538719 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 27.215 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 144 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_9327_length_13731_cov_15.800352 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; ITR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_9327_length_13731_cov_15.800352 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.9327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140688 SAMEA13538720 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738571. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538720 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 180.825 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_12_length_439879_cov_101.892911_1 Viral contig found in MAG ERR7738571_bin.336 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_12_length_439879_cov_101.892911_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_provirus.12 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140690 SAMEA13538722 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738571. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538722 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 34.5208 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 198 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_290_length_146174_cov_19.915577_1 Viral contig found in MAG ERR7738571_bin.228 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7317073170731707 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_290_length_146174_cov_19.915577_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0315825 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140691 SAMEA13538723 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738571. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538723 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 12.5374 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_563_length_104102_cov_7.036376_1 Viral contig found in MAG ERR7738571_bin.375 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_563_length_104102_cov_7.036376_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.64 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_provirus.563 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140692 SAMEA13538724 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738571. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538724 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 9.32309 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_958_length_75370_cov_5.128711_1 Viral contig found in MAG ERR7738571_bin.153 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_958_length_75370_cov_5.128711_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__UBA1234;g__UBA1234;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_provirus.958 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140693 SAMEA13538725 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738571. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538725 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 66.0352 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 108 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_1317_length_61627_cov_39.084484 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4838709677419355 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_1317_length_61627_cov_39.084484 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_provirus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140694 SAMEA13538726 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738571. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538726 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 10.2134 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 65 Number of CRISPR spacer hits supporting host taxonomy 185 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_1642_length_53493_cov_5.595365 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_1642_length_53493_cov_5.595365 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140695 SAMEA13538727 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738571. BACPHLIP temperate score 0.23805382343288484 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538727 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 25.0065 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 368 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_2030_length_45690_cov_14.496525 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3636363636363637 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_2030_length_45690_cov_14.496525 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.2030 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140696 SAMEA13538728 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738571. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538728 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 16.4751 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_2393_length_40713_cov_9.352077 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_2393_length_40713_cov_9.352077 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.2393 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140697 SAMEA13538729 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738571. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538729 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 722.488 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_2713_length_37223_cov_409.093684 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_2713_length_37223_cov_409.093684 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_virus.852 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140699 SAMEA13538731 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738571. BACPHLIP temperate score 0.0255538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538731 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 123.671 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 127 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_3997_length_27828_cov_70.889806 Viral contig found in MAG ERR7738571_bin.235 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_3997_length_27828_cov_70.889806 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.1123 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140700 SAMEA13538732 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738571. BACPHLIP temperate score 0.02673512386358416 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538732 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 23.4111 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_5021_length_23200_cov_13.565973 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_5021_length_23200_cov_13.565973 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.220 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140701 SAMEA13538733 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738571. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538733 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 2047.84 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_597_length_100710_cov_1135.381773 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.9066666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_597_length_100710_cov_1135.381773 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.457 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140702 SAMEA13538734 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacillus phage Thornton virus assembled from ERR7738571. BACPHLIP temperate score 0.03243392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538734 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 8.46585 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_8421_length_15305_cov_4.617153 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 51.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_8421_length_15305_cov_4.617153 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME237505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__HGM11412;s__HGM11412 sp900770185 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.8421 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae; Northropvirinae; Claudivirus; unclassified Claudivirus; Bacillus phage Thornton virus enrichment approach none ERS11140703 SAMEA13538735 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738572. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538735 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 16.3815 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 181 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_112_length_176715_cov_9.484267_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.979591836734694 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_112_length_176715_cov_9.484267_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME212098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_provirus.112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140705 SAMEA13538737 2133760 Siphoviridae environmental samples This sample represents an uncultured Streptococcus phage Javan284 provirus assembled from ERR7738572. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538737 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 14.8078 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 174 Number of CRISPR spacer hits supporting host taxonomy 165 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_532_length_85151_cov_8.557080_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.559322033898305 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_532_length_85151_cov_8.557080_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME212098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_provirus.513 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Streptococcus phage Javan284 virus enrichment approach none ERS11140706 SAMEA13538738 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn provirus assembled from ERR7738572. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538738 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 23.5615 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 99 Number of CRISPR spacer hits supporting host taxonomy 314 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_8_length_472117_cov_13.594306_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_8_length_472117_cov_13.594306_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0319907 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140707 SAMEA13538739 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738572. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538739 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 6.17703 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_11117_length_8205_cov_3.444267 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_11117_length_8205_cov_3.444267 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000493 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea;s__Dorea formicigenerans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.6102 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140708 SAMEA13538740 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738572. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538740 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 9.73886 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 229 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1276_length_46490_cov_5.566371 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1276_length_46490_cov_5.566371 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.1276 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140709 SAMEA13538741 2100421 uncultured Caudovirales phage This sample represents an uncultured unclassified Kayfunavirus virus assembled from ERR7738572. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538741 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 26.0449 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1665_length_39255_cov_15.090076 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6530612244897959 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1665_length_39255_cov_15.090076 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.1665 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae; Studiervirinae; Kayfunavirus; unclassified Kayfunavirus virus enrichment approach none ERS11140710 SAMEA13538742 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738572. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538742 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 8.87837 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 77 Number of CRISPR spacer hits supporting host taxonomy 639 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1804_length_36712_cov_4.954224 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1804_length_36712_cov_4.954224 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.7 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140712 SAMEA13538744 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738572. BACPHLIP temperate score 0.7349118942731276 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538744 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 12.8576 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 507 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_2208_length_31440_cov_7.474157 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_2208_length_31440_cov_7.474157 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-4420035 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140713 SAMEA13538745 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738572. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538745 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 12.1261 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_302_length_113289_cov_6.990540 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_302_length_113289_cov_6.990540 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.302 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140714 SAMEA13538746 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738572. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538746 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 14.0131 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 367 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_4714_length_16841_cov_8.072417 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_4714_length_16841_cov_8.072417 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0156279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140715 SAMEA13538747 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738572. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538747 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 96.636 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_76_length_214686_cov_56.466448 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.86 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_76_length_214686_cov_56.466448 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME150720 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp003526955 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0379585 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140716 SAMEA13538748 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738574. BACPHLIP temperate score 0.355272547781255 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538748 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 51.067 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1246_length_49334_cov_29.774672_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1246_length_49334_cov_29.774672_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738605_provirus.1182 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140718 SAMEA13538750 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738574. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538750 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 162.917 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_298_length_107450_cov_96.466570_1 Viral contig found in MAG ERR7738574_bin.50 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_298_length_107450_cov_96.466570_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0296258 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140719 SAMEA13538751 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738574. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538751 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 87.1429 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 1299 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_60_length_204646_cov_53.559400_1 Viral contig found in MAG ERR7738574_bin.108 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_60_length_204646_cov_53.559400_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745937_provirus.694 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140720 SAMEA13538752 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738574. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538752 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 57.1693 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 269 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1075_length_54417_cov_33.276445 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6071428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1075_length_54417_cov_33.276445 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738256_provirus.224 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140721 SAMEA13538753 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738574. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538753 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 151.91 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1409_length_45950_cov_91.431343 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1409_length_45950_cov_91.431343 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140722 SAMEA13538754 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738574. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538754 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 19.6202 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1693_length_41629_cov_11.843064 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42105263157894735 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_1693_length_41629_cov_11.843064 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_virus.1341 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140723 SAMEA13538755 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738574. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538755 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:46Z INSDC last update 2022-12-27T00:30:46Z INSDC status public MAG coverage depth 16.8619 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 261 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_2099_length_36602_cov_9.968296 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8387096774193549 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_2099_length_36602_cov_9.968296 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738574_virus.2099 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140724 SAMEA13538756 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738574. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538756 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 9.45692 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_2428_length_33114_cov_5.425614 Viral contig found in MAG ERR7738574_bin.93 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_2428_length_33114_cov_5.425614 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738574_virus.2428 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140725 SAMEA13538757 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll virus assembled from ERR7738574. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538757 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 13.4563 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_3339_length_26646_cov_7.821559 Viral contig found in MAG ERR7738574_bin.145 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.56 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_3339_length_26646_cov_7.821559 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_provirus.265 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11140727 SAMEA13538759 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738574. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538759 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 67.3409 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_655_length_70997_cov_40.251452 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_655_length_70997_cov_40.251452 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738155_virus.215 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140728 SAMEA13538760 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738574. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538760 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 8.34084 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_9152_length_12317_cov_4.673284 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_9152_length_12317_cov_4.673284 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.5896 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140729 SAMEA13538761 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu provirus assembled from ERR7738575. BACPHLIP temperate score 0.25195538818076474 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538761 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 8.8264 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 185 Number of CRISPR spacer hits supporting host taxonomy 561 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1536_length_42868_cov_4.744339_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1536_length_42868_cov_4.744339_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.698 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11140730 SAMEA13538762 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738575. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538762 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 81.0219 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 348 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_5_length_743725_cov_46.283211_1 Viral contig found in MAG ERR7738575_bin.139 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 20 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.5604395604395604 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_5_length_743725_cov_46.283211_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0378236 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140731 SAMEA13538763 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738575. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538763 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 33.6849 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_895_length_68621_cov_20.999095_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9583333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_895_length_68621_cov_20.999095_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_provirus.336 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11140733 SAMEA13538765 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738575. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538765 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 22.5519 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1391_length_47612_cov_12.856422 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1391_length_47612_cov_12.856422 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738575_virus.1391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140734 SAMEA13538766 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738575. BACPHLIP temperate score 0.00743392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538766 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 9.33827 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1743_length_38309_cov_5.174487 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1743_length_38309_cov_5.174487 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0327529 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140735 SAMEA13538767 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738575. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538767 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 72.2517 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1849_length_36335_cov_41.447432 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_1849_length_36335_cov_41.447432 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0281755 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140736 SAMEA13538768 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738575. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538768 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 413.129 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 120 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_2247_length_30195_cov_237.626668 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_2247_length_30195_cov_237.626668 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.1491 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140737 SAMEA13538769 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738575. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538769 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 229.33 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_3728_length_17898_cov_129.664553 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_3728_length_17898_cov_129.664553 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738575_virus.3728 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140738 SAMEA13538770 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738575. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538770 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 66.4061 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 102 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_758_length_77878_cov_37.659696 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_758_length_77878_cov_37.659696 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738575_virus.758 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140739 SAMEA13538771 2133760 Siphoviridae environmental samples This sample represents an uncultured Vegasvirus provirus assembled from ERR7738576. BACPHLIP temperate score 0.23306637662361993 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538771 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 50.5811 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1488_length_40094_cov_30.831796_1 Viral contig found in MAG ERR7738576_bin.220 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1488_length_40094_cov_30.831796_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_provirus.1488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Gochnauervirinae; Vegasvirus virus enrichment approach none ERS11140741 SAMEA13538773 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738576. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538773 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 22.8396 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 72 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_700_length_66255_cov_13.511046_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_700_length_66255_cov_13.511046_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_provirus.18 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140742 SAMEA13538774 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738576. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538774 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 188.447 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 183 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1308_length_43785_cov_108.559737 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1308_length_43785_cov_108.559737 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1308 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140743 SAMEA13538775 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738576. BACPHLIP temperate score 0.6375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538775 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 7.31278 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1442_length_40933_cov_4.083953 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1442_length_40933_cov_4.083953 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738472_bin.128 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900557405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1442 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11140744 SAMEA13538776 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738576. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538776 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 77.8386 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1552_length_39006_cov_45.097870 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1552_length_39006_cov_45.097870 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1552 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140745 SAMEA13538777 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738576. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538777 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 16.9193 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 140 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1716_length_36208_cov_10.450278 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8620689655172413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_1716_length_36208_cov_10.450278 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1716 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140747 SAMEA13538779 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738576. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538779 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 18.8515 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_3244_length_22260_cov_11.126403 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_3244_length_22260_cov_11.126403 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.3244 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140748 SAMEA13538780 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7738576. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538780 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 54.3136 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_393_length_96541_cov_32.156877 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_393_length_96541_cov_32.156877 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.393 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11140749 SAMEA13538781 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738576. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538781 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 51.5104 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 191 Number of CRISPR spacer hits supporting host taxonomy 101 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_489_length_84873_cov_31.165527 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_489_length_84873_cov_31.165527 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140750 SAMEA13538782 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738576. BACPHLIP temperate score 0.0088092263283177 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538782 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 8.4246200000000009 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_7324_length_11513_cov_4.901102 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_7324_length_11513_cov_4.901102 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.7324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140751 SAMEA13538783 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738576. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538783 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 19.858 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_932_length_55887_cov_11.789679 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5609756097560976 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_932_length_55887_cov_11.789679 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018425 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__CAG-791 sp000431495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.932 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140752 SAMEA13538784 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738577. BACPHLIP temperate score 0.877477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538784 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 23.8927 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 65 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_319_length_78337_cov_14.816611_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_319_length_78337_cov_14.816611_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140753 SAMEA13538785 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738577. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538785 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 26.0084 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_1051_length_41896_cov_15.027547 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_1051_length_41896_cov_15.027547 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_provirus.617 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140755 SAMEA13538787 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738577. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538787 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 22.0822 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_145_length_113766_cov_13.420041 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.926829268292683 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_145_length_113766_cov_13.420041 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_provirus.208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140756 SAMEA13538788 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738577. BACPHLIP temperate score 0.06384348183251046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538788 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 17.2428 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 155 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_1820_length_30467_cov_10.597203 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_1820_length_30467_cov_10.597203 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.996 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140757 SAMEA13538789 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738577. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538789 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 9.06308 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_2390_length_25959_cov_5.169500 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_2390_length_25959_cov_5.169500 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0298456 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140758 SAMEA13538790 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738577. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538790 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 3148.6 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 153 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_306_length_80952_cov_1732.150776 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5483870967741935 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_306_length_80952_cov_1732.150776 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.429 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140759 SAMEA13538791 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738577. BACPHLIP temperate score 0.22204294689013696 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538791 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 85.4184 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_41_length_189709_cov_48.572187 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_41_length_189709_cov_48.572187 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.41 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140761 SAMEA13538793 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738577. BACPHLIP temperate score 0.877477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538793 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 26.2129 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 105 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_832_length_47463_cov_16.652999 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_832_length_47463_cov_16.652999 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.832 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140762 SAMEA13538794 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738578. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538794 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 93.4494 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1067 Number of CRISPR spacer hits supporting host taxonomy 344 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_116_length_213183_cov_53.163989_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_116_length_213183_cov_53.163989_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738578_provirus.116 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140763 SAMEA13538795 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738578. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538795 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 10.4854 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 136 Number of CRISPR spacer hits supporting host taxonomy 197 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_2013_length_43459_cov_5.814577_1 Viral contig found in MAG ERR7738578_bin.256 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_2013_length_43459_cov_5.814577_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095938 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0130534 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140764 SAMEA13538796 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738578. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538796 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 66.4862 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 103 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_532_length_107225_cov_40.245632_1 Viral contig found in MAG ERR7738578_bin.7 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8717948717948718 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_532_length_107225_cov_40.245632_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738578_provirus.532 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140765 SAMEA13538797 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738578. BACPHLIP temperate score 0.17230176211453746 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538797 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 26.2121 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 351 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_897_length_78000_cov_15.162827_1 Viral contig found in MAG ERR7738578_bin.179 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_897_length_78000_cov_15.162827_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143357 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides ovatus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738578_provirus.897 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140766 SAMEA13538798 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738578. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538798 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 318.456 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 80 Number of CRISPR spacer hits supporting host taxonomy 1345 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_1329_length_59222_cov_179.710508 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_1329_length_59222_cov_179.710508 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140767 SAMEA13538799 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738578. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538799 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 9.34749 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_1727_length_48572_cov_5.158140 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_1727_length_48572_cov_5.158140 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0368262 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140768 SAMEA13538800 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738578. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538800 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 245.658 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 207 Number of CRISPR spacer hits supporting host taxonomy 259 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_2087_length_42424_cov_141.181052 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_2087_length_42424_cov_141.181052 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0308466 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140770 SAMEA13538802 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738578. BACPHLIP temperate score 0.07995594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538802 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 40.2716 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 154 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_2566_length_35224_cov_22.774518 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_2566_length_35224_cov_22.774518 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738549_virus.918 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140771 SAMEA13538803 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738578. BACPHLIP temperate score 0.06369765791341378 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538803 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 173.213 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 467 Number of CRISPR spacer hits supporting host taxonomy 558 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_2897_length_31329_cov_98.672981 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_2897_length_31329_cov_98.672981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140772 SAMEA13538804 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738578. BACPHLIP temperate score 0.0490368859781216 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538804 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 22.3522 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_3966_length_23012_cov_12.678657 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_3966_length_23012_cov_12.678657 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738578_virus.3966 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140773 SAMEA13538805 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738578. BACPHLIP temperate score 0.3492241221920916 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538805 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 13.0765 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_6298_length_13802_cov_7.397231 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_6298_length_13802_cov_7.397231 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738578_virus.6298 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140774 SAMEA13538806 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738579. BACPHLIP temperate score 0.17360358568359646 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538806 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 31.5269 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_1328_length_46309_cov_18.481398_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_1328_length_46309_cov_18.481398_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140776 SAMEA13538808 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738579. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538808 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 226.284 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_601_length_73852_cov_158.731400_1 Viral contig found in MAG ERR7738579_bin.51 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_601_length_73852_cov_158.731400_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_provirus.800 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140777 SAMEA13538809 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738579. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538809 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 21.514 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 747 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_1196_length_49481_cov_12.439985 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_1196_length_49481_cov_12.439985 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372952 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11140778 SAMEA13538810 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738579. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538810 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 45.6011 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_144_length_150236_cov_26.043008 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.734375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_144_length_150236_cov_26.043008 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738579_virus.144 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140512 SAMEA13538543 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738557. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538543 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:14Z INSDC last update 2022-12-27T00:30:14Z INSDC status public MAG coverage depth 14.6288 MAG coverage software Reads (ERR7738557) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567920) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_700_length_81334_cov_8.497373_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585810 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_12_1556__NODE_700_length_81334_cov_8.497373_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1126 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140618 SAMEA13538649 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738565. BACPHLIP temperate score 0.04343334073279703 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538649 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 12.9673 MAG coverage software Reads (ERR7738565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567905) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 105 Number of CRISPR spacer hits supporting host taxonomy 324 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_4922_length_20389_cov_7.422263 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585811 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_4922_length_20389_cov_7.422263 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140626 SAMEA13538657 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738566. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538657 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 20.0495 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 223 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1518_length_43787_cov_11.171837 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_1518_length_43787_cov_11.171837 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.1518 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140632 SAMEA13538663 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738566. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538663 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 268.011 MAG coverage software Reads (ERR7738566) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561745) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_H_9_1235__NODE_440_length_89631_cov_150.267593 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4827586206896552 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585653 sample name Hadza_MoBio_hadza-I-L_H_9_1235__NODE_440_length_89631_cov_150.267593 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738566_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140641 SAMEA13538673 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738567. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538673 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 23.5894 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_2239_length_39181_cov_13.442052 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_2239_length_39181_cov_13.442052 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.2969 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140647 SAMEA13538679 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738567. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538679 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 5.15601 MAG coverage software Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_D_14_1620__NODE_9149_length_12976_cov_2.778665 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585869 sample name Hadza_MoBio_hadza-A-D_D_14_1620__NODE_9149_length_12976_cov_2.778665 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME017973 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__UMGS124;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.3072 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140654 SAMEA13538686 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 virus assembled from ERR7738568. BACPHLIP temperate score 4.9472295514511e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538686 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:30Z INSDC last update 2022-12-27T00:30:30Z INSDC status public MAG coverage depth 51.2841 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2004_length_42341_cov_31.066794 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_2004_length_42341_cov_31.066794 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.997 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11140660 SAMEA13538692 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738568. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538692 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 34.4953 MAG coverage software Reads (ERR7738568) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567702) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_750_length_77673_cov_20.857132 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5365853658536586 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586222 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_16_2355__NODE_750_length_77673_cov_20.857132 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_virus.750 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140669 SAMEA13538701 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738569. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538701 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 14.7301 MAG coverage software Reads (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1220 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_3231_length_24333_cov_9.381473 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586171 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_3231_length_24333_cov_9.381473 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_provirus.47 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140675 SAMEA13538707 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738570. BACPHLIP temperate score 0.01110955218654152 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538707 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 18.4803 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_364_length_119275_cov_10.889931_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_364_length_119275_cov_10.889931_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_provirus.352 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140683 SAMEA13538715 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738570. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538715 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 38.9812 MAG coverage software Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_F_21_1974__NODE_3146_length_31501_cov_22.932854 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586098 sample name Hadza_MoBio_hadza-E-H_F_21_1974__NODE_3146_length_31501_cov_22.932854 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0282086 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140689 SAMEA13538721 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona provirus assembled from ERR7738571. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538721 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 11.0005 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 237 Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_1778_length_50361_cov_6.269827_1 Viral contig found in MAG ERR7738571_bin.411 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5652173913043478 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_1778_length_50361_cov_6.269827_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.1666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11140698 SAMEA13538730 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738571. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538730 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 14.8364 MAG coverage software Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_H_2_1640__NODE_319_length_139155_cov_8.310617 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 13 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.7906976744186046 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_MoBio_hadza-A-D_H_2_1640__NODE_319_length_139155_cov_8.310617 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.319 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140704 SAMEA13538736 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738572. BACPHLIP temperate score 0.00128438135477076 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538736 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 927.605 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_207_length_135363_cov_533.228649_1 Viral contig found in MAG ERR7738572_bin.274 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_207_length_135363_cov_533.228649_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.245 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140711 SAMEA13538743 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738572. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538743 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 11.4992 MAG coverage software Reads (ERR7738572) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567535) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1896_length_35323_cov_6.593713 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787403 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_3_THA1060YZ__NODE_1896_length_35323_cov_6.593713 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME256624 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-272;s__CAG-272 sp000433515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.1896 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140717 SAMEA13538749 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738574. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538749 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 29.3734 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_178_length_131002_cov_17.813007_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_178_length_131002_cov_17.813007_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_provirus.800 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140726 SAMEA13538758 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738574. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538758 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 6.45037 MAG coverage software Reads (ERR7738574) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567876) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_4561_length_21146_cov_3.502160 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_22_1305__NODE_4561_length_21146_cov_3.502160 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738614_provirus.423 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140732 SAMEA13538764 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738575. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538764 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 38.9726 MAG coverage software Reads (ERR7738575) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567530) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_124_length_229456_cov_21.976842 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 26 number of unique standard tRNAs extracted 18 percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787410 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_7_THA1072JZ__NODE_124_length_229456_cov_21.976842 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738575_virus.124 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140740 SAMEA13538772 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738576. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538772 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 123.993 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_31_length_310458_cov_76.108525_2 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_31_length_310458_cov_76.108525_2 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_provirus.66 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140746 SAMEA13538778 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738576. BACPHLIP temperate score 0.15137530562347187 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538778 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 10.3977 MAG coverage software Reads (ERR7738576) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_I_3_1743__NODE_2208_length_30018_cov_5.863331 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585986 sample name Hadza_MoBio_hadza-E-H_I_3_1743__NODE_2208_length_30018_cov_5.863331 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.2208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140754 SAMEA13538786 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738577. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538786 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 17.4637 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 284 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_1152_length_39746_cov_10.141723 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.575 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_1152_length_39746_cov_10.141723 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0347707 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140760 SAMEA13538792 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738577. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538792 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 62.8045 MAG coverage software Reads (ERR7738577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560750) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_E_23_1730__NODE_635_length_55501_cov_38.784552 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585973 sample name Hadza_MoBio_hadza-E-H_E_23_1730__NODE_635_length_55501_cov_38.784552 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0347583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140769 SAMEA13538801 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738578. BACPHLIP temperate score 0.02549472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538801 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 38.4905 MAG coverage software Reads (ERR7738578) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558882) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 333 Number of CRISPR spacer hits supporting host taxonomy 230 Submitter Id Pilot_MoBio_Fiber_A_5_1019__NODE_2396_length_37485_cov_21.828352 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9807692307692308 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383989 sample name Pilot_MoBio_Fiber_A_5_1019__NODE_2396_length_37485_cov_21.828352 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0367225 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140775 SAMEA13538807 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738579. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538807 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 62.5469 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 144 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_27_length_281367_cov_37.685350_2 Viral contig found in MAG ERR7738579_bin.196 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_27_length_281367_cov_37.685350_2 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_virus.1666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140779 SAMEA13538811 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738579. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538811 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 6.10007 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_19682_length_4277_cov_3.741667 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_19682_length_4277_cov_3.741667 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738246_bin.32 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_A;s__Ruminococcus_A faecicola vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738579_virus.19682 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140780 SAMEA13538812 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738579. BACPHLIP temperate score 0.03799472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538812 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 316.097 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_312_length_104065_cov_178.853666 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9699248120300752 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_312_length_104065_cov_178.853666 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0369190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11140781 SAMEA13538813 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738579. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538813 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 439.022 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 443 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_407_length_91712_cov_253.719900 Viral contig found in MAG ERR7738579_bin.115 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_407_length_91712_cov_253.719900 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0361433 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140782 SAMEA13538814 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738579. BACPHLIP temperate score 0.7379947229551451 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538814 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 15.3845 MAG coverage software Reads (ERR7738579) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559355) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_hadza-I-L_K_6_2620__NODE_864_length_60712_cov_8.939441 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586329 sample name Hadza_MoBio_hadza-I-L_K_6_2620__NODE_864_length_60712_cov_8.939441 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_virus.633 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140783 SAMEA13538815 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738580. BACPHLIP temperate score 0.11369765791341375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538815 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 8.7135 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1361_length_51449_cov_4.736607_1 Viral contig found in MAG ERR7738580_bin.103 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1361_length_51449_cov_4.736607_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738580_bin.103 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.1361 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140784 SAMEA13538816 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738580. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538816 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 9.26572 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1942_length_40407_cov_5.075824_1 Viral contig found in MAG ERR7738580_bin.203 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1942_length_40407_cov_5.075824_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA1829;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.2131 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140785 SAMEA13538817 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738580. BACPHLIP temperate score 0.30247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538817 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 356.617 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 195 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_366_length_109384_cov_201.050884_1 Viral contig found in MAG ERR7738580_bin.212 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_366_length_109384_cov_201.050884_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140786 SAMEA13538818 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738580. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538818 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 16.3627 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 65 Number of CRISPR spacer hits supporting host taxonomy 107 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_8_length_550033_cov_10.106561_1 Viral contig found in MAG ERR7738580_bin.128 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.323943661971831 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_8_length_550033_cov_10.106561_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738186_bin.194 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp000431775 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.8 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140787 SAMEA13538819 2133760 Siphoviridae environmental samples This sample represents an uncultured Enterobacteria phage mEp021 virus assembled from ERR7738580. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538819 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 11.9138 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1239_length_54587_cov_6.556320 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8641975308641975 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1239_length_54587_cov_6.556320 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_virus.1239 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Enterobacteria phage mEp021 virus enrichment approach none ERS11140788 SAMEA13538820 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738580. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538820 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:56Z INSDC last update 2022-12-27T00:30:56Z INSDC status public MAG coverage depth 10.0351 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 246 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1498_length_48194_cov_5.535383 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1498_length_48194_cov_5.535383 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372952 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11140789 SAMEA13538821 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738580. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538821 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 16.8028 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 322 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1732_length_43516_cov_9.376390 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_1732_length_43516_cov_9.376390 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745908_provirus.390 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140790 SAMEA13538822 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738580. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538822 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 9.88869 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_190_length_152594_cov_5.471731 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_190_length_152594_cov_5.471731 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_virus.190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140791 SAMEA13538823 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738580. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538823 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 7.49634 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2000_length_39448_cov_3.996749 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2000_length_39448_cov_3.996749 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.1684 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140792 SAMEA13538824 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738580. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538824 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 41.5653 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2198_length_36728_cov_23.301984 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2198_length_36728_cov_23.301984 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME011747 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UMGS882;s__UMGS882 sp900546385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.901 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140793 SAMEA13538825 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738580. BACPHLIP temperate score 0.4625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538825 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 16.3925 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 67 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2334_length_35123_cov_9.224277 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7096774193548387 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2334_length_35123_cov_9.224277 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140794 SAMEA13538826 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738580. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538826 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 8.78784 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2720_length_31273_cov_4.845397 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_2720_length_31273_cov_4.845397 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140795 SAMEA13538827 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738580. BACPHLIP temperate score 0.9049559471365638 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538827 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 6.17317 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_3389_length_25876_cov_3.162875 Viral contig found in MAG ERR7738580_bin.89 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_3389_length_25876_cov_3.162875 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_virus.3389 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140796 SAMEA13538828 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738580. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538828 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 54.4056 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_3906_length_22962_cov_31.769412 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_3906_length_22962_cov_31.769412 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_virus.3906 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140797 SAMEA13538829 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738580. BACPHLIP temperate score 0.04245594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538829 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 8.6612 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_5092_length_17951_cov_4.859013 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_5092_length_17951_cov_4.859013 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738575_virus.1911 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140798 SAMEA13538830 2133760 Siphoviridae environmental samples This sample represents an uncultured Enterococcus phage EF5 virus assembled from ERR7738580. BACPHLIP temperate score 0.13997797356828195 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538830 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 8.54292 MAG coverage software Reads (ERR7738580) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_681_length_79113_cov_4.695253 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 12 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787346 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_17_CHE1007SZ__NODE_681_length_79113_cov_4.695253 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0375669 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Enterococcus phage EF5 virus enrichment approach none ERS11140799 SAMEA13538831 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738581. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538831 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 13.9969 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 215 Number of CRISPR spacer hits supporting host taxonomy 330 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1025_length_72702_cov_7.848950_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1025_length_72702_cov_7.848950_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_provirus.1025 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140800 SAMEA13538832 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738581. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538832 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 112.678 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1614_length_53263_cov_63.469522_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1614_length_53263_cov_63.469522_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_provirus.881 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140801 SAMEA13538833 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738581. BACPHLIP temperate score 8.6317135549872e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538833 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 38.0985 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2563_length_38019_cov_20.773839_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2563_length_38019_cov_20.773839_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.255 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__UBA1234;g__UBA1234;s__UBA1234 sp900753135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745859_provirus.2658 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140802 SAMEA13538834 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738581. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538834 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:14Z INSDC last update 2022-12-27T19:09:14Z INSDC status public MAG coverage depth 17.4731 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_876_length_80209_cov_9.875480_1 Viral contig found in MAG ERR7738581_bin.148 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_876_length_80209_cov_9.875480_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_provirus.876 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140803 SAMEA13538835 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738581. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538835 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 12.161 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_109_length_214274_cov_6.762770 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7424242424242424 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_109_length_214274_cov_6.762770 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.109 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140804 SAMEA13538836 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738581. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538836 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 75.1197 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1357_length_59729_cov_41.349527 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1357_length_59729_cov_41.349527 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.438 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140805 SAMEA13538837 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738581. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538837 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 31.2379 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1494_length_56168_cov_17.076857 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1494_length_56168_cov_17.076857 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745859_virus.1542 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140806 SAMEA13538838 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738581. BACPHLIP temperate score 0.1193047942582454 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538838 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 32.1657 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1793_length_49562_cov_17.709508 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7352941176470589 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_1793_length_49562_cov_17.709508 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.989 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140807 SAMEA13538839 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738581. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538839 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 9.19772 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2162_length_43232_cov_4.964199 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 68.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2162_length_43232_cov_4.964199 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME158868 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900549635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.2162 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140808 SAMEA13538840 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738581. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538840 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 14.9942 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2422_length_39688_cov_8.173411 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2422_length_39688_cov_8.173411 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.2422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140809 SAMEA13538841 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738581. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538841 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 15.4049 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2778_length_35581_cov_8.419220 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_2778_length_35581_cov_8.419220 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.1612 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140810 SAMEA13538842 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738581. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538842 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 9.50253 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_3090_length_32713_cov_5.128723 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_3090_length_32713_cov_5.128723 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME234270 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740;s__UBA1740 sp900767415 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.3090 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140811 SAMEA13538843 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738581. BACPHLIP temperate score 0.08436123348017628 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538843 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 17.144 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_3788_length_27716_cov_9.150367 Viral contig found in MAG ERR7738581_bin.141 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_3788_length_27716_cov_9.150367 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.1859 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140812 SAMEA13538844 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738581. BACPHLIP temperate score 0.22815620873411188 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538844 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 8.96343 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_4513_length_23861_cov_4.450555 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_4513_length_23861_cov_4.450555 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0335721 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140813 SAMEA13538845 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738581. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538845 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 94.1323 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 1266 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_549_length_104081_cov_104.659446 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7936507936507936 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_549_length_104081_cov_104.659446 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11140814 SAMEA13538846 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738581. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538846 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 48.7989 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 284 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_660_length_93738_cov_27.204098 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_660_length_93738_cov_27.204098 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.332 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140815 SAMEA13538847 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738581. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538847 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 10.211 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_8127_length_14464_cov_5.406548 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 52.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_8127_length_14464_cov_5.406548 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738662_bin.124 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__CAG-449;s__CAG-449 sp000432895 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.8127 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140816 SAMEA13538848 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7738581. BACPHLIP temperate score 0.45 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538848 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 22.9086 MAG coverage software Reads (ERR7738581) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-A-D_K_24_1168__NODE_96_length_227439_cov_12.871359 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585592 sample name Hadza_MoBio_hadza-A-D_K_24_1168__NODE_96_length_227439_cov_12.871359 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140265 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia;s__Blautia stercoris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.46 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11140817 SAMEA13538849 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738582. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538849 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 97.0081 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 161 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_240_length_184187_cov_57.591103_1 Viral contig found in MAG ERR7738582_bin.95 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 70.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_240_length_184187_cov_57.591103_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1382 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140818 SAMEA13538850 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738582. BACPHLIP temperate score 0.00134348183251044 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538850 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 217.789 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_446_length_137250_cov_128.923935_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_446_length_137250_cov_128.923935_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_virus.95 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140819 SAMEA13538851 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738582. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538851 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 36.0929 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 105 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_858_length_89766_cov_21.900478_1 Viral contig found in MAG ERR7738582_bin.373 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_858_length_89766_cov_21.900478_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738275_provirus.129 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140820 SAMEA13538852 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738582. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538852 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 770.557 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_1255_length_68355_cov_455.201529 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_1255_length_68355_cov_455.201529 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0344814 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140821 SAMEA13538853 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738582. BACPHLIP temperate score 0.475 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538853 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 74.4049 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_1552_length_58511_cov_45.063798 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_1552_length_58511_cov_45.063798 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME011266 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696;s__UMGS1696 sp900554225 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.1552 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140822 SAMEA13538854 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738582. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538854 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 36.0286 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 93 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2108_length_45930_cov_21.412034 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2108_length_45930_cov_21.412034 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.2108 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140823 SAMEA13538855 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lugh virus assembled from ERR7738582. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538855 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 17.8749 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 994 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2401_length_41256_cov_10.542170 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5128205128205128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2401_length_41256_cov_10.542170 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME248826 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_D vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.2401 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lughvirus; Faecalibacterium virus Lugh virus enrichment approach none ERS11140824 SAMEA13538856 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738582. BACPHLIP temperate score 0.6125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538856 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 76.3464 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2673_length_37456_cov_45.385805 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2673_length_37456_cov_45.385805 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0353882 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140825 SAMEA13538857 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738582. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538857 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 19.5135 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2901_length_34975_cov_11.536105 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_2901_length_34975_cov_11.536105 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.33 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448;s__CAG-448 sp003150135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.2901 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140826 SAMEA13538858 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738582. BACPHLIP temperate score 0.03050977056944868 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538858 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 134.777 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_351_length_155323_cov_80.269295 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.6792452830188679 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_351_length_155323_cov_80.269295 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140827 SAMEA13538859 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738582. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538859 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 9.83076 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_3830_length_27650_cov_5.725238 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_3830_length_27650_cov_5.725238 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.3830 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140828 SAMEA13538860 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738582. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538860 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 146.216 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_474_length_132872_cov_86.870123 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.7317073170731707 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_474_length_132872_cov_86.870123 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.474 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11140829 SAMEA13538861 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738582. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538861 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 16.6367 MAG coverage software Reads (ERR7738582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567635) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_7161_length_15870_cov_9.874565 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS9106186 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_7_RAU0027AZ__NODE_7161_length_15870_cov_9.874565 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME258542 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__CAG-145;s__CAG-145 sp900754795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.7161 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140830 SAMEA13538862 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu provirus assembled from ERR7738583. BACPHLIP temperate score 0.3274779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538862 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 17.6063 MAG coverage software Reads (ERR7738583) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567560) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 241 Number of CRISPR spacer hits supporting host taxonomy 599 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_1377_length_39744_cov_9.918345_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787412 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_1377_length_39744_cov_9.918345_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.698 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11140831 SAMEA13538863 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738583. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538863 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 111.59 MAG coverage software Reads (ERR7738583) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567560) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_53_length_254025_cov_63.282767_1 Viral contig found in MAG ERR7738583_bin.122 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787412 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_53_length_254025_cov_63.282767_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745908_provirus.199 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140832 SAMEA13538864 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738583. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538864 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 177.374 MAG coverage software Reads (ERR7738583) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567560) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 245 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_1128_length_46624_cov_119.787355 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787412 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_1128_length_46624_cov_119.787355 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738583_virus.1128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140833 SAMEA13538865 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738583. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538865 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:17Z INSDC last update 2022-12-27T00:31:17Z INSDC status public MAG coverage depth 9.20342 MAG coverage software Reads (ERR7738583) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567560) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 211 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_1411_length_39114_cov_4.991700 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787412 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_1411_length_39114_cov_4.991700 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0300685 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140834 SAMEA13538866 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738583. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538866 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 17.7954 MAG coverage software Reads (ERR7738583) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567560) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_211_length_126009_cov_9.939086 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; ITR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787412 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_211_length_126009_cov_9.939086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME233192 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus ruminis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738583_virus.211 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140835 SAMEA13538867 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738583. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538867 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 48.1749 MAG coverage software Reads (ERR7738583) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567560) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_495_length_80647_cov_26.931488 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6458333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787412 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_495_length_80647_cov_26.931488 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745908_virus.609 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140836 SAMEA13538868 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738583. BACPHLIP temperate score 0.02241189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538868 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 83.4271 MAG coverage software Reads (ERR7738583) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567560) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_99_length_189344_cov_46.732980 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 26 number of unique standard tRNAs extracted 19 percent of BLAST hits supporting viral taxonomy 0.5147058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787412 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_15_THA1075YZ__NODE_99_length_189344_cov_46.732980 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola dorei vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0379517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140837 SAMEA13538869 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738584. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538869 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 202.241 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1437_length_57534_cov_117.791305_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1437_length_57534_cov_117.791305_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_provirus.1222 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140838 SAMEA13538870 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738584. BACPHLIP temperate score 0.3625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538870 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 319.253 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 839 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_197_length_155714_cov_195.240438_1 Viral contig found in MAG ERR7738584_bin.91 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 46.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_197_length_155714_cov_195.240438_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_provirus.197 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140839 SAMEA13538871 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738584. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538871 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 39.0951 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 340 Number of CRISPR spacer hits supporting host taxonomy 137 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_353_length_121529_cov_22.832090_1 Viral contig found in MAG ERR7738584_bin.104 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_353_length_121529_cov_22.832090_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0226686 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140840 SAMEA13538872 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe provirus assembled from ERR7738584. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538872 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 42.2955 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 500 Number of CRISPR spacer hits supporting host taxonomy 1344 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_515_length_101886_cov_25.284120_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_515_length_101886_cov_25.284120_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11140841 SAMEA13538873 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738584. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538873 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 29.5135 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_906_length_75063_cov_17.012322_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_906_length_75063_cov_17.012322_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738604_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432655 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_virus.311 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140842 SAMEA13538874 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738584. BACPHLIP temperate score 0.130873179909068 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538874 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 9.94175 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_12662_length_11755_cov_5.401610 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_12662_length_11755_cov_5.401610 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270304 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882;s__CAG-882 sp000435595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.12662 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140843 SAMEA13538875 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538875 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 677.945 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1526_length_55889_cov_387.198488 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8787878787878788 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1526_length_55889_cov_387.198488 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.1503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140844 SAMEA13538876 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.2138578943106438 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538876 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 1801.2 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1720_length_51630_cov_1757.820748 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1720_length_51630_cov_1757.820748 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.1720 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140845 SAMEA13538877 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738584. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538877 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 18.762 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 134 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1964_length_47225_cov_10.916052 Viral contig found in MAG ERR7738584_bin.181 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_1964_length_47225_cov_10.916052 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.1796 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140846 SAMEA13538878 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738584. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538878 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 33.1941 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 445 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2187_length_43948_cov_19.550705 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2187_length_43948_cov_19.550705 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.2187 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11140847 SAMEA13538879 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.08491189427312776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538879 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 65.8288 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2341_length_42165_cov_38.164394 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2341_length_42165_cov_38.164394 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.784 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140848 SAMEA13538880 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.13180120315873836 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538880 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 37.5239 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 317 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2532_length_40335_cov_21.579612 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.575 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2532_length_40335_cov_21.579612 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0347707 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140849 SAMEA13538881 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538881 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 12.3006 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2792_length_37608_cov_7.061709 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_2792_length_37608_cov_7.061709 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.2385 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140850 SAMEA13538882 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538882 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 16.7602 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_3016_length_35688_cov_9.713207 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_3016_length_35688_cov_9.713207 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.178 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1889;s__UMGS1889 sp900556055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.2463 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140851 SAMEA13538883 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538883 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 70.4152 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_32_length_277933_cov_40.856336 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.8378378378378378 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_32_length_277933_cov_40.856336 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.32 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140852 SAMEA13538884 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538884 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 10.3766 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_3841_length_30270_cov_5.922035 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.45 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_3841_length_30270_cov_5.922035 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.2220 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140853 SAMEA13538885 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538885 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 124.646 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 319 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_4339_length_27808_cov_105.096174 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_4339_length_27808_cov_105.096174 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_provirus.883 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140854 SAMEA13538886 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538886 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 9.6433700000000009 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_4817_length_25728_cov_5.459085 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_4817_length_25728_cov_5.459085 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.1803 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140855 SAMEA13538887 340016 uncultured virus This sample represents an uncultured Erwinia phage PEar6 virus assembled from ERR7738584. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538887 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 64.9202 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_55002_length_3244_cov_40.552889 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_55002_length_3244_cov_40.552889 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_virus.21413 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae; unclassified Inoviridae; Erwinia phage PEar6 virus enrichment approach none ERS11140856 SAMEA13538888 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.1884773935962332 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538888 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 7.75407 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_6062_length_21550_cov_4.402179 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_6062_length_21550_cov_4.402179 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.6062 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140857 SAMEA13538889 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538889 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 64.4063 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 146 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_830_length_78860_cov_36.967785 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_830_length_78860_cov_36.967785 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.799 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140858 SAMEA13538890 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738584. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538890 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 107.181 MAG coverage software Reads (ERR7738584) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567998) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_93_length_197854_cov_61.148445 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 12 percent of BLAST hits supporting viral taxonomy 0.5303030303030303 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585611 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_6_1188__NODE_93_length_197854_cov_61.148445 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747083_bin.116 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1994;s__UMGS1994 sp900556975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.92 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140859 SAMEA13538891 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738585. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538891 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 140.049 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 98 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_1311_length_60739_cov_94.241041_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_1311_length_60739_cov_94.241041_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140860 SAMEA13538892 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738585. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538892 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 28.6992 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 305 Number of CRISPR spacer hits supporting host taxonomy 107 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_226_length_179825_cov_17.728870_1 Viral contig found in MAG ERR7738585_bin.104 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_226_length_179825_cov_17.728870_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.79 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;s__Ruminiclostridium_E siraeum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_provirus.226 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140861 SAMEA13538893 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738585. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538893 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 67.6354 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 590 Number of CRISPR spacer hits supporting host taxonomy 163 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_43_length_343766_cov_41.781558_1 Viral contig found in MAG ERR7738585_bin.7 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 80.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_43_length_343766_cov_41.781558_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0305973 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140862 SAMEA13538894 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738585. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538894 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 240.153 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 201 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_630_length_102270_cov_157.948578_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_630_length_102270_cov_157.948578_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_provirus.630 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140863 SAMEA13538895 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738585. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538895 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 50.5126 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_952_length_78680_cov_31.046818_1 Viral contig found in MAG ERR7738585_bin.191 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_952_length_78680_cov_31.046818_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_provirus.952 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140864 SAMEA13538896 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738585. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538896 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 294.392 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_1518_length_54116_cov_181.128648 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_1518_length_54116_cov_181.128648 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_virus.1518 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11140865 SAMEA13538897 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738585. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538897 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 61.7141 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 236 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_1915_length_44897_cov_38.209772 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_1915_length_44897_cov_38.209772 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_virus.391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140866 SAMEA13538898 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738585. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538898 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 13.6237 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_2187_length_40650_cov_8.481774 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_2187_length_40650_cov_8.481774 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_virus.2187 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140867 SAMEA13538899 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738585. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538899 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 37.3804 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_2629_length_35062_cov_22.850364 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_2629_length_35062_cov_22.850364 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.326 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_virus.2629 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140868 SAMEA13538900 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738585. BACPHLIP temperate score 0.11497797356828196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538900 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 51.5338 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 125 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_3309_length_28404_cov_31.614996 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_3309_length_28404_cov_31.614996 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_virus.3309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140869 SAMEA13538901 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738585. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538901 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 10.2261 MAG coverage software Reads (ERR7738585) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567432) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 170 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_558_length_108983_cov_6.147347 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787393 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_19_RAU1029Y__NODE_558_length_108983_cov_6.147347 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019095 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002299635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738585_virus.558 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11140870 SAMEA13538902 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738586. BACPHLIP temperate score 0.5 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538902 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 47.4206 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1004_length_51380_cov_28.296045_1 Viral contig found in MAG ERR7738586_bin.180 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1004_length_51380_cov_28.296045_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.1004 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140871 SAMEA13538903 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738586. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538903 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 72.2914 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 151 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1516_length_40247_cov_42.847100_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1516_length_40247_cov_42.847100_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.1516 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140872 SAMEA13538904 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus provirus assembled from ERR7738586. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538904 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 22.0412 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_229_length_121569_cov_12.593356_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7906976744186046 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_229_length_121569_cov_12.593356_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11140873 SAMEA13538905 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738586. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538905 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 26.6045 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_36_length_264990_cov_15.854262_2 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_36_length_264990_cov_15.854262_2 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738251_virus.875 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140874 SAMEA13538906 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738586. BACPHLIP temperate score 4.9472295514511e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538906 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 9.299 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 144 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_772_length_59872_cov_5.289238_1 Viral contig found in MAG ERR7738586_bin.188 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8620689655172413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_772_length_59872_cov_5.289238_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738242_provirus.349 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140875 SAMEA13538907 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538907 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 11.7316 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 147 Number of CRISPR spacer hits supporting host taxonomy 117 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1187_length_46498_cov_7.013873 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1187_length_46498_cov_7.013873 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140876 SAMEA13538908 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538908 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 23.9835 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1519_length_40195_cov_13.851164 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1519_length_40195_cov_13.851164 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738188_virus.899 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140877 SAMEA13538909 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538909 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 9.05078 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1778_length_36797_cov_5.073094 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_1778_length_36797_cov_5.073094 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.1778 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140878 SAMEA13538910 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538910 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 6.40272 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_2276_length_32095_cov_3.816385 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_2276_length_32095_cov_3.816385 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_provirus.1739 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140879 SAMEA13538911 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538911 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 9.92745 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_2840_length_27994_cov_5.684887 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_2840_length_27994_cov_5.684887 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745403_virus.597 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140880 SAMEA13538912 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538912 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 16.0998 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_3708_length_23682_cov_9.269773 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_3708_length_23682_cov_9.269773 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.3531 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140881 SAMEA13538913 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738586. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538913 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 8.9038 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_4600_length_20837_cov_5.043786 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_4600_length_20837_cov_5.043786 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.4600 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140882 SAMEA13538914 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538914 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 19.5198 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_675_length_64588_cov_11.971307 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_675_length_64588_cov_11.971307 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738566_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.541 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140883 SAMEA13538915 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738586. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538915 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 14.7492 MAG coverage software Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_895_length_55021_cov_8.786492 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4565217391304347 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585782 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527__NODE_895_length_55021_cov_8.786492 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.186 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140884 SAMEA13538916 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738587. BACPHLIP temperate score 0.08243392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538916 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 14.9761 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1897_length_44521_cov_9.138196_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1897_length_44521_cov_9.138196_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738271_bin.229 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp002296965 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_provirus.1897 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140885 SAMEA13538917 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738587. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538917 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 18.3441 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_371_length_106676_cov_10.530239_1 Viral contig found in MAG ERR7738587_bin.244 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_371_length_106676_cov_10.530239_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_provirus.371 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140886 SAMEA13538918 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738587. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538918 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 52.2881 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_705_length_76378_cov_33.599953_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7407407407407407 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_705_length_76378_cov_33.599953_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_provirus.705 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140887 SAMEA13538919 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.08986784140969165 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538919 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 46.9502 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1144_length_59343_cov_27.151368 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8648648648648649 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1144_length_59343_cov_27.151368 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.1144 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140888 SAMEA13538920 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.6 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538920 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 17.1601 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1462_length_52219_cov_10.551341 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1462_length_52219_cov_10.551341 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.170 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.1462 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140889 SAMEA13538921 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7738587. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538921 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 17.2455 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1802_length_45826_cov_10.335046 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6578947368421053 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1802_length_45826_cov_10.335046 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_provirus.1539 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11140890 SAMEA13538922 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538922 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 8.62319 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1973_length_43432_cov_4.860616 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_1973_length_43432_cov_4.860616 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746349_bin.99 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1883;f__UMGS1883;g__UMGS1883;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.1973 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140891 SAMEA13538923 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.4125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538923 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 21.7983 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_2254_length_40162_cov_12.498865 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_2254_length_40162_cov_12.498865 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.212 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia;s__Romboutsia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.2254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140892 SAMEA13538924 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538924 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 7.80591 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_2443_length_38164_cov_4.234857 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_2443_length_38164_cov_4.234857 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__UMGS124;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.2094 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140893 SAMEA13538925 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538925 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 18.0827 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 287 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_260_length_127234_cov_10.381387 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_260_length_127234_cov_10.381387 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140894 SAMEA13538926 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538926 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 50.8049 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_2847_length_34485_cov_29.259591 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_2847_length_34485_cov_29.259591 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME011266 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696;s__UMGS1696 sp900554225 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.2847 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140895 SAMEA13538927 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538927 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 10.8437 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_3240_length_31749_cov_6.193420 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_3240_length_31749_cov_6.193420 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.2306 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140896 SAMEA13538928 2100421 uncultured Caudovirales phage This sample represents an uncultured unclassified Henuseptimavirus virus assembled from ERR7738587. BACPHLIP temperate score 0.0323237885462555 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538928 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 10.2195 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_3884_length_27928_cov_5.828337 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5588235294117647 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_3884_length_27928_cov_5.828337 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0312761 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Drexlerviridae; Tempevirinae; Henuseptimavirus; unclassified Henuseptimavirus virus enrichment approach none ERS11140897 SAMEA13538929 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738587. BACPHLIP temperate score 0.05250921161364957 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538929 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:10Z INSDC last update 2022-12-27T00:30:10Z INSDC status public MAG coverage depth 16.2354 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_4431_length_25532_cov_9.703202 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_4431_length_25532_cov_9.703202 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738277_bin.130 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger sp900554145 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140898 SAMEA13538930 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538930 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 14.1538 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_555_length_86763_cov_8.478612 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_555_length_86763_cov_8.478612 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738178_virus.64 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140899 SAMEA13538931 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.46888544708081953 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538931 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 8.51487 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_7008_length_18104_cov_4.869751 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_7008_length_18104_cov_4.869751 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.7008 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140900 SAMEA13538932 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738587. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538932 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 16.8682 MAG coverage software Reads (ERR7738587) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567913) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_869_length_68264_cov_10.043733 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 26 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585897 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_20_1653__NODE_869_length_68264_cov_10.043733 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140901 SAMEA13538933 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738588. BACPHLIP temperate score 0.864977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538933 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 43.6975 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1210_length_62896_cov_23.858928_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1210_length_62896_cov_23.858928_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140902 SAMEA13538934 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu provirus assembled from ERR7738588. BACPHLIP temperate score 0.30247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538934 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 44.3822 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 274 Number of CRISPR spacer hits supporting host taxonomy 568 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1670_length_51920_cov_23.772062_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1670_length_51920_cov_23.772062_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.698 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11140903 SAMEA13538935 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738588. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538935 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 63.115 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2581_length_38195_cov_35.150296_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2581_length_38195_cov_35.150296_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.1657 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140904 SAMEA13538936 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738588. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538936 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 53.5071 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 69 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_4_length_773851_cov_29.079685_1 Viral contig found in MAG ERR7738588_bin.304 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_4_length_773851_cov_29.079685_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_provirus.36 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140905 SAMEA13538937 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738588. BACPHLIP temperate score 0.6125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538937 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 40.5982 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_876_length_76172_cov_22.298324_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_876_length_76172_cov_22.298324_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_provirus.996 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140906 SAMEA13538938 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538938 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:11Z INSDC last update 2022-12-27T00:30:11Z INSDC status public MAG coverage depth 5.75814 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_11562_length_10772_cov_2.973539 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.25 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_11562_length_10772_cov_2.973539 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.11562 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140907 SAMEA13538939 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738588. BACPHLIP temperate score 4.9472295514511e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538939 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 236.219 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1482_length_55861_cov_122.263050 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1482_length_55861_cov_122.263050 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746757_bin.199 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436;s__UBA1436 sp900541355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.1482 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140908 SAMEA13538940 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538940 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 39.2543 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 97 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1954_length_46812_cov_21.283428 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_1954_length_46812_cov_21.283428 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738167_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFHK01;s__SFHK01 sp004556395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1815 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140909 SAMEA13538941 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538941 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 34.5826 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2309_length_41521_cov_17.829119 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2309_length_41521_cov_17.829119 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME171351 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella;s__Veillonella parvula_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.2309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140910 SAMEA13538942 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738588. BACPHLIP temperate score 0.02619765791341376 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538942 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 56.2767 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2559_length_38460_cov_30.038481 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2559_length_38460_cov_30.038481 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_provirus.1044 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140911 SAMEA13538943 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538943 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 9.03718 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 183 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2808_length_35921_cov_4.822676 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_2808_length_35921_cov_4.822676 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125893 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger formicilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0352455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140912 SAMEA13538944 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538944 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 42.2969 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_3055_length_33786_cov_22.716189 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_3055_length_33786_cov_22.716189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745432_bin.107 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA733;s__UBA733 sp900767825 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.3055 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140913 SAMEA13538945 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538945 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 57.03 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_371_length_122069_cov_29.822611 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_371_length_122069_cov_29.822611 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738630_bin.77 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_virus.200 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140914 SAMEA13538946 336724 Myoviridae environmental samples This sample represents an uncultured Yongloolinvirus virus assembled from ERR7738588. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538946 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 7.43283 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_4402_length_25192_cov_3.845670 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_4402_length_25192_cov_3.845670 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.4402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Yongloolinvirus virus enrichment approach none ERS11140915 SAMEA13538947 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.07564699712046227 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538947 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 35.1368 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_4971_length_22614_cov_18.951147 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_4971_length_22614_cov_18.951147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.328 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1750;g__UBA7102;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.4971 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140916 SAMEA13538948 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738588. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538948 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 20.249 MAG coverage software Reads (ERR7738588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561697) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_O_4_1196__NODE_6601_length_17778_cov_10.500141 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585619 sample name Hadza_MoBio_hadza-A-D_O_4_1196__NODE_6601_length_17778_cov_10.500141 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145587 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A;s__Slackia_A isoflavoniconvertens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.6601 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140917 SAMEA13538949 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738591. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538949 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 27.9388 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1013_length_58073_cov_16.901459_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1013_length_58073_cov_16.901459_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_provirus.1013 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140918 SAMEA13538950 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738591. BACPHLIP temperate score 0.0920154185022027 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538950 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 13.5204 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1818_length_40216_cov_8.134283_1 Viral contig found in MAG ERR7738591_bin.186 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1818_length_40216_cov_8.134283_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_provirus.1818 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140919 SAMEA13538951 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738591. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538951 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 102.902 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1002 Number of CRISPR spacer hits supporting host taxonomy 359 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_653_length_75457_cov_63.367127_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_653_length_75457_cov_63.367127_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME150720 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp003526955 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_provirus.653 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140920 SAMEA13538952 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538952 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 8.119 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 484 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1158_length_53251_cov_4.575150 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.47368421052631576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1158_length_53251_cov_4.575150 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME184321 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.1158 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140921 SAMEA13538953 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538953 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 199.463 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 347 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1520_length_44862_cov_116.829608 Viral contig found in MAG ERR7738591_bin.222 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1520_length_44862_cov_116.829608 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.1976 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140922 SAMEA13538954 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538954 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 2503.26 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 137 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1628_length_42751_cov_1449.825186 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1628_length_42751_cov_1449.825186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.1628 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140923 SAMEA13538955 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538955 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 355.048 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1699_length_41852_cov_208.359186 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5357142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1699_length_41852_cov_208.359186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.1699 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140924 SAMEA13538956 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538956 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 50.9894 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1851_length_39715_cov_33.249306 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_1851_length_39715_cov_33.249306 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001507 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruthenibacterium;s__Ruthenibacterium lactatiformans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.1851 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140925 SAMEA13538957 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538957 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 172.275 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_197_length_144752_cov_101.775048 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_197_length_144752_cov_101.775048 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.242 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__HGM11416;s__HGM11416 sp900766495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.197 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140926 SAMEA13538958 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538958 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 83.6389 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_2159_length_36377_cov_49.679559 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_2159_length_36377_cov_49.679559 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.2159 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140927 SAMEA13538959 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538959 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 30.6721 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 181 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_2348_length_34283_cov_18.906625 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_2348_length_34283_cov_18.906625 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.2348 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140928 SAMEA13538960 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538960 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 10.3296 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_2729_length_30992_cov_6.340417 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_2729_length_30992_cov_6.340417 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.2729 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140929 SAMEA13538961 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538961 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 27.7707 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_325_length_108084_cov_17.306313 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5686274509803921 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_325_length_108084_cov_17.306313 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.325 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140930 SAMEA13538962 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538962 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 204.198 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_42_length_257669_cov_126.627605 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_42_length_257669_cov_126.627605 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.13 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140931 SAMEA13538963 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538963 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 14.0674 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_4763_length_20577_cov_8.393317 Viral contig found in MAG ERR7738591_bin.320 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_4763_length_20577_cov_8.393317 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.4763 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140932 SAMEA13538964 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538964 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 1918.51 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_5522_length_18302_cov_1120.129931 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_5522_length_18302_cov_1120.129931 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.5522 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140933 SAMEA13538965 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738591. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538965 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 21.3741 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_6668_length_15931_cov_12.574240 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_6668_length_15931_cov_12.574240 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.6668 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140934 SAMEA13538966 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738591. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538966 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 10.6215 MAG coverage software Reads (ERR7738591) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560351) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_K_7_1773__NODE_943_length_60576_cov_6.265674 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585995 sample name Hadza_MoBio_hadza-E-H_K_7_1773__NODE_943_length_60576_cov_6.265674 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738240_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__Firm-11;s__Firm-11 sp900548145 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_virus.943 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140935 SAMEA13538967 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738592. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538967 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 25.4432 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_180_length_151537_cov_14.575261_1 Viral contig found in MAG ERR7738592_bin.90 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_180_length_151537_cov_14.575261_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_provirus.172 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140936 SAMEA13538968 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738592. BACPHLIP temperate score 0.31762027361593803 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538968 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 73.2496 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_444_length_91757_cov_42.032101_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_444_length_91757_cov_42.032101_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0295015 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11140937 SAMEA13538969 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738592. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538969 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 168.151 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 406 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_74_length_218151_cov_96.109770_1_1 Viral contig found in MAG ERR7738592_bin.71 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_74_length_218151_cov_96.109770_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME249912 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__Megasphaera sp000417505 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_provirus.74 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140938 SAMEA13538970 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738592. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538970 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 98.8137 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_1035_length_50296_cov_70.590553 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_1035_length_50296_cov_70.590553 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_virus.1035 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11140939 SAMEA13538971 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738592. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538971 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 8.23073 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_1274_length_43920_cov_4.496887 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_1274_length_43920_cov_4.496887 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_virus.1274 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140940 SAMEA13538972 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738592. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13538972 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-28T19:46:12Z INSDC status public MAG coverage depth 36.9588 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 124 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_1705_length_34975_cov_21.033870 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_1705_length_34975_cov_21.033870 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0289566 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140941 SAMEA13538973 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738592. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538973 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 13.845 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 590 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_2269_length_27512_cov_7.972845 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_2269_length_27512_cov_7.972845 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_virus.2269 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11140942 SAMEA13538974 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738592. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538974 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 99.8714 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 54 Number of CRISPR spacer hits supporting host taxonomy 149 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_491_length_86784_cov_59.874324 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6052631578947368 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_491_length_86784_cov_59.874324 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_virus.491 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140943 SAMEA13538975 340016 uncultured virus This sample represents an uncultured unclassified Inoviridae virus assembled from ERR7738592. BACPHLIP temperate score 0.15236784140969165 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538975 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 16.8677 MAG coverage software Reads (ERR7738592) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 84 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_9681_length_7172_cov_10.820155 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787404 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_21_THA1063YZ__NODE_9681_length_7172_cov_10.820155 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.9812 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae; unclassified Inoviridae virus enrichment approach none ERS11140944 SAMEA13538976 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738593. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538976 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 30.4261 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_2_length_615939_cov_17.474767_1 Viral contig found in MAG ERR7738593_bin.144 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.717391304347826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_2_length_615939_cov_17.474767_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738612_provirus.2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140945 SAMEA13538977 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738593. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538977 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 12.7516 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_544_length_76905_cov_7.344900_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_544_length_76905_cov_7.344900_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.790 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140946 SAMEA13538978 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738593. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538978 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 17.2838 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_890_length_58355_cov_10.013092_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.525 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_890_length_58355_cov_10.013092_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.1639 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140947 SAMEA13538979 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738593. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538979 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 238.068 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 161 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_1326_length_45727_cov_139.337963 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_1326_length_45727_cov_139.337963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_virus.1326 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140948 SAMEA13538980 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738593. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538980 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 11.3534 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_1454_length_43297_cov_6.671356 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7297297297297297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_1454_length_43297_cov_6.671356 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_virus.1454 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140949 SAMEA13538981 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738593. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538981 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 18.9283 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_1730_length_38318_cov_10.982453 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_1730_length_38318_cov_10.982453 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_virus.1730 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140950 SAMEA13538982 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738593. BACPHLIP temperate score 0.03869765791341377 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538982 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 54.3419 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 245 Number of CRISPR spacer hits supporting host taxonomy 503 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_2286_length_31606_cov_31.338038 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_2286_length_31606_cov_31.338038 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11140951 SAMEA13538983 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738593. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538983 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 192.264 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_327_length_100390_cov_110.309721 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.990990990990991 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_327_length_100390_cov_110.309721 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.346 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11140952 SAMEA13538984 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738593. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538984 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 5.82834 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 117 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_5557_length_16572_cov_3.051046 Viral contig found in MAG ERR7738593_bin.117 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_5557_length_16572_cov_3.051046 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0278013 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140953 SAMEA13538985 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738593. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538985 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 8.12377 MAG coverage software Reads (ERR7738593) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560155) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_D_16_2189__NODE_860_length_59526_cov_4.547965 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586150 sample name Hadza_MoBio_hadza-E-H_D_16_2189__NODE_860_length_59526_cov_4.547965 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0360712 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140954 SAMEA13538986 926697 uncultured Microviridae This sample represents an uncultured unclassified Microviridae provirus assembled from ERR7738594. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538986 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 9.90562 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_11492_length_9580_cov_5.565506_1 Viral contig found in MAG ERR7738594_bin.29 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_11492_length_9580_cov_5.565506_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738594_bin.29 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-314;g__CAG-1435;s__CAG-1435 sp900769665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_provirus.2959 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae virus enrichment approach none ERS11140955 SAMEA13538987 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738594. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538987 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 20.652 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_2065_length_40619_cov_11.980193_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_2065_length_40619_cov_11.980193_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140956 SAMEA13538988 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738594. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538988 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 10.6095 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_488_length_98079_cov_6.224975_1 Viral contig found in MAG ERR7738594_bin.224 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_488_length_98079_cov_6.224975_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140957 SAMEA13538989 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738594. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538989 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 34.718 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_779_length_75063_cov_19.239538_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_779_length_75063_cov_19.239538_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738604_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432655 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_virus.311 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140958 SAMEA13538990 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738594. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538990 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 33.4489 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 134 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1170_length_58991_cov_18.976101 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1170_length_58991_cov_18.976101 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.1796 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140959 SAMEA13538991 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738594. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538991 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 308.823 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 307 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1379_length_52402_cov_174.229431 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1379_length_52402_cov_174.229431 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738198_virus.99 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140960 SAMEA13538992 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738594. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538992 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 119.813 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1522_length_49343_cov_64.989689 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1522_length_49343_cov_64.989689 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.189 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1522 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140961 SAMEA13538993 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738594. BACPHLIP temperate score 0.25247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538993 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 60.4445 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_178_length_155160_cov_34.010240 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_178_length_155160_cov_34.010240 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.32 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140962 SAMEA13538994 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738594. BACPHLIP temperate score 0.3875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538994 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 107.109 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1869_length_43253_cov_69.632296 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_1869_length_43253_cov_69.632296 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME172369 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-917;g__CAG-349;s__CAG-349 sp003539515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1869 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140963 SAMEA13538995 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738594. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538995 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 29.2416 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_2090_length_40370_cov_16.097610 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_2090_length_40370_cov_16.097610 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.2090 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140964 SAMEA13538996 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738594. BACPHLIP temperate score 0.18068787764054067 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538996 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 25.3454 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_22712_length_5205_cov_14.327223 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_22712_length_5205_cov_14.327223 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.22712 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11140965 SAMEA13538997 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7738594. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538997 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 45.0633 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_248_length_137919_cov_25.017680 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_248_length_137919_cov_25.017680 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.248 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11140966 SAMEA13538998 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738594. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538998 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 9.88783 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 113 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_2785_length_32610_cov_5.369778 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_2785_length_32610_cov_5.369778 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11140967 SAMEA13538999 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lugh virus assembled from ERR7738594. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13538999 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 7.75689 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_3053_length_30560_cov_4.229538 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9629629629629628 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_3053_length_30560_cov_4.229538 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.3053 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lughvirus; Faecalibacterium virus Lugh virus enrichment approach none ERS11140968 SAMEA13539000 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738594. BACPHLIP temperate score 0.03326220277569512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539000 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 16.427 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_360_length_115485_cov_8.981942 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 12 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_360_length_115485_cov_8.981942 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.63 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140969 SAMEA13539001 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738594. BACPHLIP temperate score 0.05905891240983968 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539001 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 88.2056 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 123 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_4206_length_23647_cov_65.063683 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_4206_length_23647_cov_65.063683 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_provirus.1808 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140970 SAMEA13539002 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738594. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539002 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:19Z INSDC last update 2022-12-27T00:30:19Z INSDC status public MAG coverage depth 15.8278 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_452_length_102504_cov_8.674851 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9777777777777776 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_452_length_102504_cov_8.674851 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.500 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140971 SAMEA13539003 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738594. BACPHLIP temperate score 0.12488986784140972 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539003 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 29.5911 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_4991_length_20502_cov_16.049547 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_4991_length_20502_cov_16.049547 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738580_bin.236 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668;s__UMGS1668 sp900553955 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.6153 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140972 SAMEA13539004 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738594. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539004 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 13.6773 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_6079_length_17155_cov_7.780712 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_6079_length_17155_cov_7.780712 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.4536 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140973 SAMEA13539005 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738594. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539005 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 129.648 MAG coverage software Reads (ERR7738594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561686) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_O_6_1198__NODE_849_length_71542_cov_71.168922 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 74.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585621 sample name Hadza_MoBio_hadza-A-D_O_6_1198__NODE_849_length_71542_cov_71.168922 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.849 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140974 SAMEA13539006 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738595. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539006 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 29.5384 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1597_length_41406_cov_17.455419_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1597_length_41406_cov_17.455419_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME086787 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C;s__Ruminococcus_C sp000433635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_provirus.1597 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140975 SAMEA13539007 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738595. BACPHLIP temperate score 0.4375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539007 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 19.3498 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_612_length_75126_cov_11.336833_1 Viral contig found in MAG ERR7738595_bin.271 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_612_length_75126_cov_11.336833_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143191 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__Olsenella_E sp003609875 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.1794 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140976 SAMEA13539008 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738595. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539008 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 56.1247 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1126_length_52548_cov_32.451659 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.525 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1126_length_52548_cov_32.451659 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.1126 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140977 SAMEA13539009 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll virus assembled from ERR7738595. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539009 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 19.659300000000002 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 82 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1378_length_45791_cov_11.951131 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1378_length_45791_cov_11.951131 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.1378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11140978 SAMEA13539010 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738595. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539010 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 17.4144 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1154 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1671_length_40224_cov_11.198097 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1671_length_40224_cov_11.198097 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.1671 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140979 SAMEA13539011 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738595. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539011 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 21.77 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1887_length_37045_cov_13.134251 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_1887_length_37045_cov_13.134251 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.2098 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140980 SAMEA13539012 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738595. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539012 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 32.6014 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 107 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_2120_length_34110_cov_23.972674 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_2120_length_34110_cov_23.972674 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_provirus.197 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140981 SAMEA13539013 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738595. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539013 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 9.31283 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_2462_length_30668_cov_5.169037 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9130434782608696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_2462_length_30668_cov_5.169037 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.2769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140982 SAMEA13539014 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738595. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539014 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 20.7857 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_3112_length_25730_cov_19.091334 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_3112_length_25730_cov_19.091334 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.3112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140983 SAMEA13539015 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738595. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539015 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 8.81743 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_3808_length_22295_cov_5.028130 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_3808_length_22295_cov_5.028130 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738561_bin.41 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__UBA1191 sp900066305 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.4207 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140984 SAMEA13539016 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738595. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539016 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 24.0756 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 245 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_543_length_80774_cov_14.102098 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_543_length_80774_cov_14.102098 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.592 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140985 SAMEA13539017 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738595. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539017 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 59.8177 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_6527_length_15081_cov_34.961744 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_6527_length_15081_cov_34.961744 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000493 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea;s__Dorea formicigenerans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.7258 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140986 SAMEA13539018 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738595. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539018 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 10.3398 MAG coverage software Reads (ERR7738595) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560321) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_MoBio_hadza-E-H_G_21_1740__NODE_775_length_66058_cov_5.882057 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585983 sample name Hadza_MoBio_hadza-E-H_G_21_1740__NODE_775_length_66058_cov_5.882057 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.775 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140987 SAMEA13539019 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738596. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539019 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 16.2675 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1345_length_54340_cov_9.182666_1 Viral contig found in MAG ERR7738596_bin.98 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1345_length_54340_cov_9.182666_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.345 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;s__Anaerobutyricum hallii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_provirus.1345 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140988 SAMEA13539020 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus provirus assembled from ERR7738596. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539020 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 15.7244 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_225_length_133866_cov_8.915785_1 Viral contig found in MAG ERR7738596_bin.228 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_225_length_133866_cov_8.915785_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_provirus.225 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11140989 SAMEA13539021 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738596. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539021 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 38.9949 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_455_length_96004_cov_22.073368_1 Viral contig found in MAG ERR7738596_bin.112 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_455_length_96004_cov_22.073368_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738555_provirus.57 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140990 SAMEA13539022 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738596. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539022 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 37.6786 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1005_length_63491_cov_21.744378 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9318181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1005_length_63491_cov_21.744378 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME192801 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp000432135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745881_virus.550 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140991 SAMEA13539023 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738596. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539023 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 84.766 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 710 Number of CRISPR spacer hits supporting host taxonomy 242 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1407_length_52817_cov_52.874251 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1407_length_52817_cov_52.874251 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.1407 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140992 SAMEA13539024 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738596. BACPHLIP temperate score 0.2138578943106438 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539024 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 3501.24 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1615_length_49126_cov_1960.410039 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_1615_length_49126_cov_1960.410039 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.1720 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11140993 SAMEA13539025 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738596. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539025 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:23Z INSDC last update 2022-12-27T00:30:23Z INSDC status public MAG coverage depth 26.5212 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_2158_length_41548_cov_15.924140 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_2158_length_41548_cov_15.924140 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.1746 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140994 SAMEA13539026 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738596. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539026 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 12.8775 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_2447_length_38713_cov_7.327234 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_2447_length_38713_cov_7.327234 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.2447 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140995 SAMEA13539027 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738596. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539027 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 174.293 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 53 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_3036_length_33678_cov_101.577304 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_3036_length_33678_cov_101.577304 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.3036 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140996 SAMEA13539028 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738596. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539028 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 14.2722 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_3493_length_30852_cov_8.154703 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_3493_length_30852_cov_8.154703 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.3493 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11140997 SAMEA13539029 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738596. BACPHLIP temperate score 0.04000921161364958 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539029 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 9.50398 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_4271_length_26935_cov_5.319086 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_4271_length_26935_cov_5.319086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738277_bin.130 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger sp900554145 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.4271 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11140998 SAMEA13539030 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738596. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539030 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 148.486 MAG coverage software Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_MoBio_hadza-A-D_D_21_1577__NODE_7438_length_18327_cov_85.957479 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585826 sample name Hadza_MoBio_hadza-A-D_D_21_1577__NODE_7438_length_18327_cov_85.957479 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.3878 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11140999 SAMEA13539031 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738597. BACPHLIP temperate score 0.18953744493392077 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539031 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 525.977 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_119_length_218523_cov_295.050287_1 Viral contig found in MAG ERR7738597_bin.108 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; HMM-based (lower-bound) completeness score 55.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8214285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_119_length_218523_cov_295.050287_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738597_provirus.119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141000 SAMEA13539032 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738597. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539032 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 16.8964 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 155 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_2148_length_38371_cov_9.491200_1 Viral contig found in MAG ERR7738597_bin.64 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_2148_length_38371_cov_9.491200_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738562_provirus.1508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141001 SAMEA13539033 2133760 Siphoviridae environmental samples This sample represents an uncultured Cbastvirus provirus assembled from ERR7738597. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539033 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 36.7252 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_34_length_332261_cov_20.906109_1 Viral contig found in MAG ERR7738597_bin.143 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_34_length_332261_cov_20.906109_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738597_provirus.34 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cbastvirus virus enrichment approach none ERS11141002 SAMEA13539034 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738597. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539034 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 105.937 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 197 Number of CRISPR spacer hits supporting host taxonomy 1492 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_770_length_87355_cov_64.447260_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6888888888888889 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_770_length_87355_cov_64.447260_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0342940 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141003 SAMEA13539035 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738597. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539035 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 7.95152 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_1751_length_46290_cov_4.360937 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_1751_length_46290_cov_4.360937 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0341914 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141004 SAMEA13539036 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738597. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539036 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 181.79 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1147 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_1988_length_41340_cov_106.493275 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_1988_length_41340_cov_106.493275 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME283914 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900066565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738597_virus.1988 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141005 SAMEA13539037 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738597. BACPHLIP temperate score 0.05958149779735685 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539037 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 97.6132 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 78 Number of CRISPR spacer hits supporting host taxonomy 399 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_2274_length_36463_cov_55.866295 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_2274_length_36463_cov_55.866295 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_provirus.1602 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141006 SAMEA13539038 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738597. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13539038 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-28T19:46:13Z INSDC status public MAG coverage depth 36.3019 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 136 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_2876_length_29465_cov_21.054580 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5757575757575758 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_2876_length_29465_cov_21.054580 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0311326 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11141007 SAMEA13539039 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738597. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539039 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 50.566 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_3932_length_20789_cov_31.277762 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_3932_length_20789_cov_31.277762 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0264879 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141008 SAMEA13539040 336724 Myoviridae environmental samples This sample represents an uncultured Phage DP SC_6_H4_2017 virus assembled from ERR7738597. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539040 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 197.029 MAG coverage software Reads (ERR7738597) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558864) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Pilot_MoBio_Fiber_C_21_7002__NODE_928_length_77657_cov_107.628384 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5303030303030303 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383922 sample name Pilot_MoBio_Fiber_C_21_7002__NODE_928_length_77657_cov_107.628384 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000838 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella;s__Barnesiella intestinihominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0351244 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Phage DP SC_6_H4_2017 virus enrichment approach none ERS11141009 SAMEA13539041 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738598. BACPHLIP temperate score 0.2123898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539041 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 137.544 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 264 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_163_length_163269_cov_80.650430_1 Viral contig found in MAG ERR7738598_bin.207 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_163_length_163269_cov_80.650430_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141010 SAMEA13539042 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738598. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539042 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 13.655 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2312_length_40751_cov_7.754020_1 Viral contig found in MAG ERR7738598_bin.9 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2312_length_40751_cov_7.754020_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_provirus.2312 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141011 SAMEA13539043 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738598. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539043 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 14.9192 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_5471_length_22742_cov_8.768454_1 Viral contig found in MAG ERR7738598_bin.160 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_5471_length_22742_cov_8.768454_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.2722 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141012 SAMEA13539044 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738598. BACPHLIP temperate score 0.03714174109185703 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539044 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 11.8665 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_111_length_192926_cov_6.550254 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.5409836065573771 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_111_length_192926_cov_6.550254 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.111 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141013 SAMEA13539045 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738598. BACPHLIP temperate score 0.02349942002795121 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539045 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 25.5129 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_12691_length_12186_cov_14.292995 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_12691_length_12186_cov_14.292995 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.12691 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11141014 SAMEA13539046 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 0.11513032049760293 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539046 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 231.728 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_1545_length_53217_cov_128.847309 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_1545_length_53217_cov_128.847309 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME155972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D;s__Haemophilus_D parainfluenzae_K vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.1545 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141015 SAMEA13539047 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738598. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539047 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 76.8003 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_1876_length_46745_cov_42.710423 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6944444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_1876_length_46745_cov_42.710423 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.1876 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141016 SAMEA13539048 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738598. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539048 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 54.4975 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2136_length_43011_cov_30.289537 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2136_length_43011_cov_30.289537 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME157359 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA3388;s__UBA3388 sp900545215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_provirus.172 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141017 SAMEA13539049 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539049 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 13.3642 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2286_length_41089_cov_7.167341 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2286_length_41089_cov_7.167341 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.2286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141018 SAMEA13539050 2133760 Siphoviridae environmental samples This sample represents an uncultured Psavirus virus assembled from ERR7738598. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539050 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 72.0987 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2552_length_37997_cov_38.875580 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2552_length_37997_cov_38.875580 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.2552 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Psavirus virus enrichment approach none ERS11141019 SAMEA13539051 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539051 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 69.4854 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 190 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2855_length_35490_cov_38.409482 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_2855_length_35490_cov_38.409482 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.191 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141020 SAMEA13539052 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738598. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539052 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 11.3278 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_32059_length_5648_cov_6.903787 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_32059_length_5648_cov_6.903787 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.32059 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11141021 SAMEA13539053 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539053 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 105.955 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_3564_length_30818_cov_56.823916 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_3564_length_30818_cov_56.823916 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.3564 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141022 SAMEA13539054 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539054 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 7.42184 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 355 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_4627_length_25603_cov_4.130024 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_4627_length_25603_cov_4.130024 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.4627 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141023 SAMEA13539055 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 0.11569612348054097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539055 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 12.6451 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_5467_length_22752_cov_6.700728 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_5467_length_22752_cov_6.700728 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0341385 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141024 SAMEA13539056 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539056 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 7.59647 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_685_length_83795_cov_8.183963 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_685_length_83795_cov_8.183963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.685 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141025 SAMEA13539057 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738598. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539057 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 34.036 MAG coverage software Reads (ERR7738598) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560385) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-E-H_K_17_1778__NODE_849_length_74736_cov_18.612558 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586000 sample name Hadza_MoBio_hadza-E-H_K_17_1778__NODE_849_length_74736_cov_18.612558 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.849 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141026 SAMEA13539058 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona provirus assembled from ERR7738599. BACPHLIP temperate score 0.15247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539058 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 21.5064 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 1777 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1471_length_50526_cov_12.601974_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9552238805970148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1471_length_50526_cov_12.601974_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738256_virus.291 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11141027 SAMEA13539059 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738599. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539059 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 16.9607 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_290_length_118488_cov_10.126340_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 70 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_290_length_118488_cov_10.126340_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_provirus.290 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141028 SAMEA13539060 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738599. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539060 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 15.6871 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_549_length_88671_cov_9.574903_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_549_length_88671_cov_9.574903_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_virus.588 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141029 SAMEA13539061 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738599. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539061 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 10.4854 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_987_length_63119_cov_5.688160_1 Viral contig found in MAG ERR7738599_bin.136 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_987_length_63119_cov_5.688160_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_provirus.351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141030 SAMEA13539062 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738599. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539062 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 11.8945 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 177 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1106_length_59389_cov_6.877883 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1106_length_59389_cov_6.877883 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141031 SAMEA13539063 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738599. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539063 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 35.9736 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1377_length_52640_cov_21.271693 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1377_length_52640_cov_21.271693 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11141032 SAMEA13539064 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738599. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539064 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 10.8755 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 552 Number of CRISPR spacer hits supporting host taxonomy 1373 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1617_length_47669_cov_5.994159 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5490196078431373 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1617_length_47669_cov_5.994159 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11141033 SAMEA13539065 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738599. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539065 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:13Z INSDC last update 2022-12-27T19:09:13Z INSDC status public MAG coverage depth 11.7613 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 290 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1881_length_43199_cov_6.858518 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_1881_length_43199_cov_6.858518 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.1881 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141034 SAMEA13539066 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738599. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539066 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 21.3026 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_2098_length_40145_cov_15.854422 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_2098_length_40145_cov_15.854422 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.2098 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141035 SAMEA13539067 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738599. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539067 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 31.63 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_238_length_132279_cov_18.097608 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.5957446808510638 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_238_length_132279_cov_18.097608 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_virus.88 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141036 SAMEA13539068 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738599. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539068 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 64.8741 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_2586_length_34545_cov_40.587385 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_2586_length_34545_cov_40.587385 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_provirus.17 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141037 SAMEA13539069 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738599. BACPHLIP temperate score 0.19297827089674777 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539069 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:26Z INSDC last update 2022-12-27T00:30:26Z INSDC status public MAG coverage depth 27.155 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_3635_length_27107_cov_15.332149 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_3635_length_27107_cov_15.332149 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.3635 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141038 SAMEA13539070 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738599. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539070 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 8.24484 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_4496_length_23055_cov_4.782662 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_4496_length_23055_cov_4.782662 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746739_virus.193 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141039 SAMEA13539071 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738599. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539071 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 216.872 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_526_length_90834_cov_119.326851 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_526_length_90834_cov_119.326851 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.526 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141040 SAMEA13539072 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738599. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539072 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 417.264 MAG coverage software Reads (ERR7738599) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560520) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_hadza-E-H_K_14_1915__NODE_768_length_72856_cov_242.696190 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586058 sample name Hadza_MoBio_hadza-E-H_K_14_1915__NODE_768_length_72856_cov_242.696190 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11141041 SAMEA13539073 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738600. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539073 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 79.4663 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_148_length_142957_cov_46.530676_1 Viral contig found in MAG ERR7738600_bin.253 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_148_length_142957_cov_46.530676_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0256792 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141042 SAMEA13539074 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738600. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539074 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 7.93652 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 333 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_2818_length_25073_cov_4.441871_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_2818_length_25073_cov_4.441871_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0365260 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141043 SAMEA13539075 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738600. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539075 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 27.4599 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 685 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_72_length_189808_cov_16.794441_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7246376811594203 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_72_length_189808_cov_16.794441_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_provirus.72 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141044 SAMEA13539076 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539076 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 14.7726 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 318 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_115_length_159495_cov_8.866107 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.7285714285714285 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_115_length_159495_cov_8.866107 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.115 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141045 SAMEA13539077 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539077 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 24.2133 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 935 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_1385_length_38844_cov_14.033430 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_1385_length_38844_cov_14.033430 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1385 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141046 SAMEA13539078 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539078 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 13.697 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_1533_length_36528_cov_8.189021 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_1533_length_36528_cov_8.189021 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME158868 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900549635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1533 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141047 SAMEA13539079 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539079 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 7.64549 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_1731_length_34067_cov_4.394851 Viral contig found in MAG ERR7738600_bin.273 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_1731_length_34067_cov_4.394851 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738571_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag1;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141048 SAMEA13539080 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539080 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 16.1994 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_2133_length_29875_cov_9.687999 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_2133_length_29875_cov_9.687999 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.2503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141049 SAMEA13539081 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7738600. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539081 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 23.6751 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_26_length_257472_cov_13.857344 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.515625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_26_length_257472_cov_13.857344 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.13 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11141050 SAMEA13539082 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0.04316671142296685 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539082 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 18.8265 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_3430_length_22207_cov_11.177542 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_3430_length_22207_cov_11.177542 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME086787 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C;s__Ruminococcus_C sp000433635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738660_provirus.182 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141051 SAMEA13539083 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539083 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 19.289 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_4379_length_18836_cov_11.662455 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_4379_length_18836_cov_11.662455 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738198_virus.716 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141052 SAMEA13539084 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738600. BACPHLIP temperate score 0.7649779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539084 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 45.186 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_673_length_60283_cov_27.181261 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_673_length_60283_cov_27.181261 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.673 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141053 SAMEA13539085 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738600. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539085 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 47.2707 MAG coverage software Reads (ERR7738600) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567950) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_9157_length_11138_cov_25.966741 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_12_1518__NODE_9157_length_11138_cov_25.966741 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.9157 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11141054 SAMEA13539086 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738601. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539086 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 49.2179 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 174 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1567_length_44448_cov_29.731807_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1567_length_44448_cov_29.731807_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1308 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141055 SAMEA13539087 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738601. BACPHLIP temperate score 0.07750921161364957 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539087 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 65.8548 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 68 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_290_length_118358_cov_35.543435_1 Viral contig found in MAG ERR7738601_bin.235 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_290_length_118358_cov_35.543435_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.1761 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141056 SAMEA13539088 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738601. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539088 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 20.7765 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_39_length_271971_cov_12.246835_1 Viral contig found in MAG ERR7738601_bin.110 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_39_length_271971_cov_12.246835_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_provirus.39 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141057 SAMEA13539089 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738601. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539089 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 17.3547 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_878_length_64101_cov_10.396804_1 Viral contig found in MAG ERR7738601_bin.233 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_878_length_64101_cov_10.396804_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_provirus.878 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141058 SAMEA13539090 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539090 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 29.5036 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1157_length_53855_cov_16.839916 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1157_length_53855_cov_16.839916 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_provirus.1357 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141059 SAMEA13539091 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539091 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 17.4492 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1453_length_46592_cov_10.828055 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.935483870967742 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1453_length_46592_cov_10.828055 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1453 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141060 SAMEA13539092 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539092 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 176.558 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 69 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1822_length_40268_cov_109.030703 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1822_length_40268_cov_109.030703 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141061 SAMEA13539093 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738601. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539093 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 77.2612 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1906_length_39119_cov_45.922314 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_1906_length_39119_cov_45.922314 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.3103 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141062 SAMEA13539094 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.07359817362478667 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539094 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 37.7039 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_2101_length_36470_cov_22.527711 Viral contig found in MAG ERR7738601_bin.76 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_2101_length_36470_cov_22.527711 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.2101 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141063 SAMEA13539095 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539095 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 97.399 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_2278_length_34351_cov_56.751298 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9310344827586208 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_2278_length_34351_cov_56.751298 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001213 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B;s__Lachnoclostridium_B sp900066555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.2278 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141064 SAMEA13539096 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738601. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539096 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 10.6093 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_2630_length_31121_cov_6.169244 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_2630_length_31121_cov_6.169244 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738222_bin.69 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__CAG-269 sp900556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.2630 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141065 SAMEA13539097 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7738601. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539097 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 30.2547 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_33_length_294248_cov_17.110473 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5272727272727272 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_33_length_294248_cov_17.110473 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.6 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11141066 SAMEA13539098 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7738601. BACPHLIP temperate score 0.08312057094440387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539098 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 6.70758 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_3807_length_23469_cov_3.637868 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_3807_length_23469_cov_3.637868 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.1505 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11141067 SAMEA13539099 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus virus assembled from ERR7738601. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539099 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 51.2898 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_4233_length_21625_cov_30.433729 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_4233_length_21625_cov_30.433729 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745963_bin.410 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp001916075 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.4233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11141068 SAMEA13539100 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.06720782038701123 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539100 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 23.8542 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_5029_length_18895_cov_13.525986 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_5029_length_18895_cov_13.525986 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.2701 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11141069 SAMEA13539101 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539101 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 17.7249 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 70 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_716_length_71840_cov_10.507741 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6170212765957447 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_716_length_71840_cov_10.507741 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141070 SAMEA13539102 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738601. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539102 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 348.449 MAG coverage software Reads (ERR7738601) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_O_16_1933__NODE_891_length_63605_cov_200.202981 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4888888888888889 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586074 sample name Hadza_MoBio_hadza-E-H_O_16_1933__NODE_891_length_63605_cov_200.202981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745858_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__UMGS1670;s__UMGS1670 sp900553995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141071 SAMEA13539103 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738602. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539103 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 18.8943 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1554_length_48513_cov_11.381183_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1554_length_48513_cov_11.381183_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745975_bin.324 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__UMGS124;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.1554 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141072 SAMEA13539104 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738602. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539104 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 23.0946 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_2182_length_38898_cov_14.348368_1 Viral contig found in MAG ERR7738602_bin.358 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_2182_length_38898_cov_14.348368_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.2182 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141073 SAMEA13539105 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738602. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539105 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 40.2829 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_4383_length_24804_cov_24.670522_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_4383_length_24804_cov_24.670522_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_virus.1581 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141074 SAMEA13539106 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738602. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539106 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 12.7909 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_644_length_83033_cov_7.812069_1 Viral contig found in MAG ERR7738602_bin.175 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_644_length_83033_cov_7.812069_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738167_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFHK01;s__SFHK01 sp004556395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.644 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141075 SAMEA13539107 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539107 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 38.1746 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1192_length_57417_cov_24.009383 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9318181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1192_length_57417_cov_24.009383 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.224 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__Ruminococcus sp900540005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.1271 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141076 SAMEA13539108 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539108 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 10.376 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 93 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1448_length_50804_cov_6.072900 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1448_length_50804_cov_6.072900 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.1328 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141077 SAMEA13539109 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539109 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 23.1217 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1935_length_42398_cov_13.980104 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_1935_length_42398_cov_13.980104 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091217 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973;s__UMGS973 sp900547295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.1935 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141078 SAMEA13539110 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539110 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 33.3169 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_2263_length_38085_cov_20.040465 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_2263_length_38085_cov_20.040465 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.2263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141079 SAMEA13539111 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539111 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 39.5798 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_2566_length_35418_cov_24.831272 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_2566_length_35418_cov_24.831272 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745975_bin.137 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;s__CAG-488 sp000434055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.2566 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141080 SAMEA13539112 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539112 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 27.4173 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 97 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_3393_length_29407_cov_17.950631 Viral contig found in MAG ERR7738602_bin.251 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_3393_length_29407_cov_17.950631 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.3044 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141081 SAMEA13539113 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539113 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 14.1929 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_4635_length_23929_cov_8.409274 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_4635_length_23929_cov_8.409274 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.2423 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141082 SAMEA13539114 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539114 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 10.7916 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_6175_length_19589_cov_6.409338 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_6175_length_19589_cov_6.409338 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_provirus.652 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141083 SAMEA13539115 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738602. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539115 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 24.9466 MAG coverage software Reads (ERR7738602) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567849) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_942_length_66422_cov_15.028849 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585781 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_4_1526__NODE_942_length_66422_cov_15.028849 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0361518 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141084 SAMEA13539116 336724 Myoviridae environmental samples This sample represents an uncultured Eganvirus provirus assembled from ERR7738603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539116 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 214.483 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_1457_length_44074_cov_119.298907_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5952380952380952 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_1457_length_44074_cov_119.298907_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.1457 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Peduovirinae; Eganvirus virus enrichment approach none ERS11141085 SAMEA13539117 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539117 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 99.2931 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 270 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_295_length_121500_cov_60.316999_1 Viral contig found in MAG ERR7738603_bin.42 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_295_length_121500_cov_60.316999_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0340593 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141086 SAMEA13539118 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738603. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539118 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 10.8535 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_535_length_87259_cov_5.932647_1 Viral contig found in MAG ERR7738603_bin.65 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_535_length_87259_cov_5.932647_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.535 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141087 SAMEA13539119 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738603. BACPHLIP temperate score 0.45 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539119 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 15.6344 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_900_length_62726_cov_8.732558_1 Viral contig found in MAG ERR7738603_bin.176 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_900_length_62726_cov_8.732558_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.900 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141088 SAMEA13539120 2100421 uncultured Caudovirales phage This sample represents an uncultured Vectrevirus virus assembled from ERR7738603. BACPHLIP temperate score 0.00128438135477076 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539120 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 10.1755 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_1494_length_43407_cov_5.535033 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7884615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_1494_length_43407_cov_5.535033 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.1494 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae; Molineuxvirinae; Vectrevirus virus enrichment approach none ERS11141089 SAMEA13539121 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738603. BACPHLIP temperate score 0.06265694085351817 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539121 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 10.5949 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_1891_length_35972_cov_5.692771 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_1891_length_35972_cov_5.692771 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746794_bin.16 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia;s__Rothia sp902373285 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.1891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141090 SAMEA13539122 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus virus assembled from ERR7738603. BACPHLIP temperate score 0.17230176211453746 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539122 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 65.1702 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 143 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_2746_length_26917_cov_37.166542 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_2746_length_26917_cov_37.166542 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0261292 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11141091 SAMEA13539123 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738603. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539123 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 28.2846 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_369_length_107447_cov_15.884251 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.66 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_369_length_107447_cov_15.884251 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257836 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273;s__CAG-273 sp003534295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.369 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141092 SAMEA13539124 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738603. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539124 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 219.446 MAG coverage software Reads (ERR7738603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560031) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_P_19_2149__NODE_5316_length_14654_cov_123.774508 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586135 sample name Hadza_MoBio_hadza-E-H_P_19_2149__NODE_5316_length_14654_cov_123.774508 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000426 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A sp900066205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.8840 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11141093 SAMEA13539125 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738604. BACPHLIP temperate score 0.05270140052539582 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539125 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 61.2765 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1342_length_45737_cov_35.011870_1 Viral contig found in MAG ERR7738604_bin.164 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1342_length_45737_cov_35.011870_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141094 SAMEA13539126 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738604. BACPHLIP temperate score 0.0378845907965548 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539126 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 35.0788 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_212_length_138333_cov_19.865677_1 Viral contig found in MAG ERR7738604_bin.249 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5142857142857142 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_212_length_138333_cov_19.865677_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746349_bin.313 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95;s__CAG-95 sp000436115 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141095 SAMEA13539127 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738604. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539127 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 18.1833 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_695_length_71838_cov_10.428185_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_695_length_71838_cov_10.428185_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_provirus.695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141096 SAMEA13539128 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738604. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539128 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 38.2386 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 141 Number of CRISPR spacer hits supporting host taxonomy 155 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1119_length_52141_cov_23.833897 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1119_length_52141_cov_23.833897 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.726 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141097 SAMEA13539129 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738604. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539129 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 78.609 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1301_length_46940_cov_44.452446 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1301_length_46940_cov_44.452446 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.394 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141098 SAMEA13539130 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738604. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539130 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 166.464 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 386 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1558_length_41664_cov_95.313608 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6176470588235294 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1558_length_41664_cov_95.313608 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_virus.1558 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141099 SAMEA13539131 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738604. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539131 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 200.342 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 234 Number of CRISPR spacer hits supporting host taxonomy 144 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1833_length_37050_cov_113.109458 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_1833_length_37050_cov_113.109458 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.1890 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141100 SAMEA13539132 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738604. BACPHLIP temperate score 0.13243392070484583 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539132 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 9.05109 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_2253_length_31977_cov_5.413480 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_2253_length_31977_cov_5.413480 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.1046 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141101 SAMEA13539133 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738604. BACPHLIP temperate score 0.0880538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539133 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 95.1653 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 155 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_2687_length_28184_cov_53.362685 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_2687_length_28184_cov_53.362685 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.1123 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141102 SAMEA13539134 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738604. BACPHLIP temperate score 0.8574339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539134 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 16.3335 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 287 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_4158_length_20338_cov_9.393613 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_4158_length_20338_cov_9.393613 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.328 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141103 SAMEA13539135 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738604. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539135 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:12Z INSDC last update 2022-12-27T19:09:12Z INSDC status public MAG coverage depth 88.7682 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_591_length_80092_cov_48.567094 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7575757575757576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_591_length_80092_cov_48.567094 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_virus.591 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141104 SAMEA13539136 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738604. BACPHLIP temperate score 0.07360955218654153 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539136 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 80.4329 MAG coverage software Reads (ERR7738604) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560302) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_H_22_2297__NODE_894_length_60931_cov_44.082640 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586176 sample name Hadza_MoBio_hadza-E-H_H_22_2297__NODE_894_length_60931_cov_44.082640 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.661 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141105 SAMEA13539137 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738605. BACPHLIP temperate score 0.10914096916299568 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539137 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 44.1896 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 79 Number of CRISPR spacer hits supporting host taxonomy 167 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1273_length_51462_cov_27.744848_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1273_length_51462_cov_27.744848_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_provirus.1602 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141106 SAMEA13539138 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738605. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539138 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 12.1048 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1831_length_41922_cov_7.409750_1 Viral contig found in MAG ERR7738605_bin.282 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1831_length_41922_cov_7.409750_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_provirus.719 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141107 SAMEA13539139 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738605. BACPHLIP temperate score 0.802477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539139 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 19.9613 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 87 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_343_length_102139_cov_12.353275_1 Viral contig found in MAG ERR7738605_bin.246 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_343_length_102139_cov_12.353275_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME108259 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900313215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738433_provirus.31 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141108 SAMEA13539140 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738605. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539140 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 715.765 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 98 Number of CRISPR spacer hits supporting host taxonomy 2162 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_56_length_202820_cov_538.454990_1 Viral contig found in MAG ERR7738605_bin.267 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.8032786885245902 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_56_length_202820_cov_538.454990_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738221_virus.272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141109 SAMEA13539141 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis provirus assembled from ERR7738605. BACPHLIP temperate score 0.2149779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539141 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 97.6561 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 299 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_859_length_63874_cov_58.645673_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_859_length_63874_cov_58.645673_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738605_provirus.859 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11141110 SAMEA13539142 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738605. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539142 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 2261.18 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1575 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1047_length_57889_cov_1315.322113 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1047_length_57889_cov_1315.322113 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738256_virus.457 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141111 SAMEA13539143 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738605. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539143 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 76.4486 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1397_length_48503_cov_46.963800 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1397_length_48503_cov_46.963800 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738616_bin.92 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.1152 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141112 SAMEA13539144 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738605. BACPHLIP temperate score 0.18963559754245787 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539144 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 25.9525 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1673_length_44253_cov_15.517747 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; HMM-based (lower-bound) completeness score 70.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_1673_length_44253_cov_15.517747 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738605_virus.1673 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141113 SAMEA13539145 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738605. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539145 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:37Z INSDC last update 2022-12-27T00:30:37Z INSDC status public MAG coverage depth 9.73597 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_2254_length_36506_cov_5.620577 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_2254_length_36506_cov_5.620577 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.1253 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141114 SAMEA13539146 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738605. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539146 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 12.9635 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 120 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_2780_length_31433_cov_7.856742 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9642857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_2780_length_31433_cov_7.856742 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.1517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141115 SAMEA13539147 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738605. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539147 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 14.0935 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_351_length_101283_cov_8.319388 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 11 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_351_length_101283_cov_8.319388 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738550_virus.509 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141116 SAMEA13539148 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738605. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539148 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 7.1963 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_4682_length_21362_cov_4.152549 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_4682_length_21362_cov_4.152549 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.1786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141117 SAMEA13539149 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738605. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539149 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 14.4147 MAG coverage software Reads (ERR7738605) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567948) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_802_length_66348_cov_8.593653 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8780487804878049 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585722 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_24_1307__NODE_802_length_66348_cov_8.593653 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738574_virus.721 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141118 SAMEA13539150 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738606. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539150 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 69.4046 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_118_length_151101_cov_39.360148_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 11 percent of BLAST hits supporting viral taxonomy 0.6307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_118_length_151101_cov_39.360148_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_provirus.118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141119 SAMEA13539151 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738606. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539151 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 24.5994 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_152_length_133641_cov_14.371470_1 Viral contig found in MAG ERR7738606_bin.201 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9838709677419356 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_152_length_133641_cov_14.371470_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738530_bin.33 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium sp900539945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_provirus.152 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141120 SAMEA13539152 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738606. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539152 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 153.663 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 220 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_30_length_247433_cov_87.161585_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_30_length_247433_cov_87.161585_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140265 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia;s__Blautia stercoris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_provirus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141121 SAMEA13539153 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738606. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539153 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 200.462 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 80 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_579_length_75165_cov_115.419681_1 Viral contig found in MAG ERR7738606_bin.21 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_579_length_75165_cov_115.419681_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.2792 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141122 SAMEA13539154 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738606. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539154 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 80.8277 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 82 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_960_length_58273_cov_47.876572_1 Viral contig found in MAG ERR7738606_bin.17 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 67.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_960_length_58273_cov_47.876572_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141123 SAMEA13539155 340016 uncultured virus This sample represents an uncultured Klebsiella phage P-K7R virus assembled from ERR7738606. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539155 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 135.869 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1215_length_51750_cov_78.186790 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6447368421052632 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1215_length_51750_cov_78.186790 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME239725 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola plebeius_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.1208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Klebsiella phage P-K7R virus enrichment approach none ERS11141124 SAMEA13539156 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539156 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 22.6945 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1483_length_46513_cov_12.928827 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1483_length_46513_cov_12.928827 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.1412 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141125 SAMEA13539157 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539157 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 344.44 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1693_length_43152_cov_194.993685 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.4583333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1693_length_43152_cov_194.993685 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141126 SAMEA13539158 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539158 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 44.6457 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1864_length_40988_cov_25.732590 Viral contig found in MAG ERR7738606_bin.24 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7037037037037037 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_1864_length_40988_cov_25.732590 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738534_bin.96 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820;s__UMGS1820 sp900555375 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.1864 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141127 SAMEA13539159 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539159 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 17.4738 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 276 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_2093_length_38448_cov_10.701467 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_2093_length_38448_cov_10.701467 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.2093 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141128 SAMEA13539160 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539160 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 12.7609 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_2566_length_33914_cov_7.219375 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_2566_length_33914_cov_7.219375 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.345 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;s__Anaerobutyricum hallii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.2566 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141129 SAMEA13539161 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738606. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539161 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 26.1157 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_2947_length_31055_cov_15.394990 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_2947_length_31055_cov_15.394990 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.1999 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141130 SAMEA13539162 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539162 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 73.631 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_3662_length_26940_cov_43.686111 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_3662_length_26940_cov_43.686111 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.3662 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141131 SAMEA13539163 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 0.24217479228380095 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539163 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 8.02313 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 427 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_4459_length_23674_cov_4.556003 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_4459_length_23674_cov_4.556003 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.62 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141132 SAMEA13539164 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7738606. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539164 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 4.69001 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_59361_length_2834_cov_2.286543 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_59361_length_2834_cov_2.286543 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME258268 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp003522105 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.59361 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11141133 SAMEA13539165 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539165 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 17.9163 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_778_length_64331_cov_10.602966 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 52.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_778_length_64331_cov_10.602966 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.778 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141134 SAMEA13539166 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738606. BACPHLIP temperate score 0.575 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539166 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 28.479 MAG coverage software Reads (ERR7738606) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567847) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_9394_length_13951_cov_17.513406 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_18_1651__NODE_9394_length_13951_cov_17.513406 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745963_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.8602 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141135 SAMEA13539167 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus provirus assembled from ERR7738607. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539167 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:38Z INSDC last update 2022-12-27T00:30:38Z INSDC status public MAG coverage depth 15.0674 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1416_length_50335_cov_8.525309_1 Viral contig found in MAG ERR7738607_bin.63 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1416_length_50335_cov_8.525309_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA6414;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_provirus.225 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11141136 SAMEA13539168 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738607. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539168 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 173.712 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 626 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1885_length_42251_cov_102.252525_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1885_length_42251_cov_102.252525_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_provirus.1885 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141137 SAMEA13539169 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738607. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539169 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 40.7801 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 476 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_387_length_106011_cov_23.372043_1 Viral contig found in MAG ERR7738607_bin.46 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_387_length_106011_cov_23.372043_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_virus.1289 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141138 SAMEA13539170 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738607. BACPHLIP temperate score 0.0160654993231054 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539170 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:47Z INSDC last update 2022-12-27T00:30:47Z INSDC status public MAG coverage depth 12.6756 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_797_length_72477_cov_7.019171_1 Viral contig found in MAG ERR7738607_bin.55 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_797_length_72477_cov_7.019171_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1124;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_provirus.797 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141139 SAMEA13539171 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738607. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539171 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 121.779 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1043_length_61500_cov_67.430393 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9142857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1043_length_61500_cov_67.430393 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738591_bin.256 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UMGS1603;s__UMGS1603 sp900553265 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.1043 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141140 SAMEA13539172 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738607. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539172 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 105.65 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1267_length_54096_cov_59.536811 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5142857142857142 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1267_length_54096_cov_59.536811 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738148_bin.20 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A;s__Selenomonas_A sp900769615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.1267 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141141 SAMEA13539173 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539173 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 12.4438 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 131 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1560_length_47261_cov_7.212572 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1560_length_47261_cov_7.212572 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.1560 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141142 SAMEA13539174 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738607. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539174 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 71.891 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 797 Number of CRISPR spacer hits supporting host taxonomy 893 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1798_length_43528_cov_52.926883 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1798_length_43528_cov_52.926883 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.235 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141143 SAMEA13539175 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539175 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 9.13342 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1976_length_41014_cov_5.483279 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_1976_length_41014_cov_5.483279 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.1976 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141144 SAMEA13539176 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539176 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 19.0571 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_2181_length_38544_cov_11.270180 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4705882352941176 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_2181_length_38544_cov_11.270180 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.2181 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141145 SAMEA13539177 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539177 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 64.9989 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 145 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_2409_length_36086_cov_36.437030 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_2409_length_36086_cov_36.437030 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738250_virus.615 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141146 SAMEA13539178 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539178 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 10.3374 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_2592_length_34427_cov_5.713013 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_2592_length_34427_cov_5.713013 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.2592 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141147 SAMEA13539179 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539179 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 15.7556 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_3146_length_30192_cov_9.170347 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_3146_length_30192_cov_9.170347 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.3146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141148 SAMEA13539180 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738607. BACPHLIP temperate score 0.25247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539180 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 22.4243 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 194 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_4290_length_24064_cov_13.430483 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_4290_length_24064_cov_13.430483 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.4290 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141149 SAMEA13539181 340016 uncultured virus This sample represents an uncultured Ralstonia phage 1 NP-2014 virus assembled from ERR7738607. BACPHLIP temperate score 0.15957970773951435 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539181 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 6.72401 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_49745_length_3295_cov_3.876321 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_49745_length_3295_cov_3.876321 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.49745 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae; unclassified Inoviridae; Ralstonia phage 1 NP-2014 virus enrichment approach none ERS11141150 SAMEA13539182 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738607. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539182 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 89.9802 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 196 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_577_length_86578_cov_52.088646 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_577_length_86578_cov_52.088646 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.577 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141151 SAMEA13539183 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539183 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 358.99 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_632_length_82638_cov_210.010186 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.525 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_632_length_82638_cov_210.010186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.632 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141152 SAMEA13539184 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738607. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539184 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 33.1755 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_803_length_72039_cov_19.487480 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_803_length_72039_cov_19.487480 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.803 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11141153 SAMEA13539185 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738607. BACPHLIP temperate score 0.00247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539185 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 20.9282 MAG coverage software Reads (ERR7738607) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560761) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 99 Submitter Id Hadza_MoBio_hadza-E-H_E_15_1726__NODE_9727_length_12905_cov_12.191496 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585969 sample name Hadza_MoBio_hadza-E-H_E_15_1726__NODE_9727_length_12905_cov_12.191496 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.9727 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141154 SAMEA13539186 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738608. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539186 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 282.863 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 77 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_1491_length_59155_cov_169.901875_1 Viral contig found in MAG ERR7738608_bin.175 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 89.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_1491_length_59155_cov_169.901875_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738143_provirus.773 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141155 SAMEA13539187 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738608. BACPHLIP temperate score 0.15247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539187 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 94.0294 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 389 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_182_length_188243_cov_62.793608_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_182_length_188243_cov_62.793608_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_provirus.918 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141156 SAMEA13539188 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738608. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539188 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 30.8841 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_31_length_365069_cov_18.616112_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 16 number of unique standard tRNAs extracted 12 percent of BLAST hits supporting viral taxonomy 0.603448275862069 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_31_length_365069_cov_18.616112_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_virus.76 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141157 SAMEA13539189 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738608. BACPHLIP temperate score 0.575 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539189 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 13.6361 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 250 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_559_length_108783_cov_8.111144_1 Viral contig found in MAG ERR7738608_bin.157 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_559_length_108783_cov_8.111144_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.160 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141158 SAMEA13539190 2100421 uncultured Caudovirales phage This sample represents an uncultured Schitoviridae virus assembled from ERR7738608. BACPHLIP temperate score 0.11513032049760293 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539190 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 30.5861 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 328 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_1037_length_74939_cov_18.432315 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_1037_length_74939_cov_18.432315 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.669 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Schitoviridae virus enrichment approach none ERS11141159 SAMEA13539191 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738608. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539191 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 8.4951 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 289 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_1550_length_57310_cov_4.920745 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_1550_length_57310_cov_4.920745 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.269 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141160 SAMEA13539192 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738608. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539192 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 21.6272 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_196_length_181453_cov_12.990192 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8103448275862069 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_196_length_181453_cov_12.990192 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738249_virus.71 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141161 SAMEA13539193 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738608. BACPHLIP temperate score 0.09273040577452842 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539193 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 16.9725 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_2316_length_42164_cov_10.258108 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_2316_length_42164_cov_10.258108 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0280225 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141162 SAMEA13539194 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738608. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539194 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 12.9287 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_2651_length_37875_cov_7.694878 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_2651_length_37875_cov_7.694878 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738569_virus.1419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141163 SAMEA13539195 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738608. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539195 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 12.2007 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 1155 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_3086_length_33869_cov_7.282759 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8928571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_3086_length_33869_cov_7.282759 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_provirus.2663 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141164 SAMEA13539196 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738608. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539196 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 36.5595 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_4553_length_24450_cov_22.219915 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_4553_length_24450_cov_22.219915 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738179_virus.1723 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141165 SAMEA13539197 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Ceridwen virus assembled from ERR7738608. BACPHLIP temperate score 0.07747797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539197 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 8.41085 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_6195_length_18546_cov_5.007147 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_6195_length_18546_cov_5.007147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.4576 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Butyrivibrio virus Ceridwen virus enrichment approach none ERS11141166 SAMEA13539198 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738608. BACPHLIP temperate score 0.2693548984968848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539198 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 15.8893 MAG coverage software Reads (ERR7738608) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_I_17_2476__NODE_9001_length_13264_cov_9.375066 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586250 sample name Hadza_MoBio_hadza-I-L_I_17_2476__NODE_9001_length_13264_cov_9.375066 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.110 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__HGM11416;s__HGM11416 sp900768525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.6311 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11141167 SAMEA13539199 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738609. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539199 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 727.554 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 195 Number of CRISPR spacer hits supporting host taxonomy 134 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_258_length_127313_cov_412.919818_1 Viral contig found in MAG ERR7738609_bin.115 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 39.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_258_length_127313_cov_412.919818_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0370468 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141168 SAMEA13539200 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738609. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539200 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 86.3558 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 87 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_60_length_242047_cov_47.859987_1 Viral contig found in MAG ERR7738609_bin.136 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_60_length_242047_cov_47.859987_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141169 SAMEA13539201 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738609. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539201 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 12.7135 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 145 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_1251_length_51615_cov_6.947883 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4074074074074074 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_1251_length_51615_cov_6.947883 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738609_virus.1251 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141170 SAMEA13539202 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738609. BACPHLIP temperate score 0.17695805183806096 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539202 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 53.8127 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_1424_length_47689_cov_29.865433 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_1424_length_47689_cov_29.865433 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME117056 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella sp002299315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745397_virus.290 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141171 SAMEA13539203 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738609. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539203 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 20.587 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 578 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_1783_length_40737_cov_11.520389 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_1783_length_40737_cov_11.520389 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141172 SAMEA13539204 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738609. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539204 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 82.8681 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 153 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_2141_length_35756_cov_46.140643 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_2141_length_35756_cov_46.140643 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738609_virus.2141 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141173 SAMEA13539205 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738609. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539205 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 18.5469 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_2701_length_29570_cov_9.205337 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_2701_length_29570_cov_9.205337 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900542795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.539 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141174 SAMEA13539206 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738609. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539206 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 9.19716 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_3084_length_26469_cov_4.989429 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_3084_length_26469_cov_4.989429 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746757_virus.1092 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141175 SAMEA13539207 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738609. BACPHLIP temperate score 0.02549472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539207 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:48Z INSDC last update 2022-12-27T00:30:48Z INSDC status public MAG coverage depth 70.7636 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_381_length_103597_cov_39.253149 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_381_length_103597_cov_39.253149 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0369090 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11141176 SAMEA13539208 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738609. BACPHLIP temperate score 0.17270013350281002 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539208 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 83.786 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_4937_length_17845_cov_45.108397 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_4937_length_17845_cov_45.108397 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738609_virus.4937 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141177 SAMEA13539209 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738609. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539209 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 214.697 MAG coverage software Reads (ERR7738609) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560346) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_K_1_1770__NODE_8239_length_11604_cov_115.228148 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585992 sample name Hadza_MoBio_hadza-E-H_K_1_1770__NODE_8239_length_11604_cov_115.228148 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745970_bin.19 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900551985 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.8863 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11141178 SAMEA13539210 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738610. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539210 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 25.5419 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_1189_length_41908_cov_14.764266_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_1189_length_41908_cov_14.764266_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0256792 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141179 SAMEA13539211 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738610. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539211 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 34.5102 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 141 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_378_length_76660_cov_19.971286_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_378_length_76660_cov_19.971286_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141180 SAMEA13539212 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738610. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539212 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 116.283 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 212 Number of CRISPR spacer hits supporting host taxonomy 128 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_71_length_143974_cov_66.608484_1 Viral contig found in MAG ERR7738610_bin.17 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_71_length_143974_cov_66.608484_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268072 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella stercorea vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0318509 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141181 SAMEA13539213 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738610. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539213 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 124.57 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_1049_length_45386_cov_71.013618 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_1049_length_45386_cov_71.013618 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738569_provirus.178 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141182 SAMEA13539214 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738610. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539214 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 18.6441 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 123 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_1309_length_39272_cov_10.582549 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_1309_length_39272_cov_10.582549 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.1309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141183 SAMEA13539215 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738610. BACPHLIP temperate score 0.5875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539215 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 184.59 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 725 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_160_length_108784_cov_106.859199 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_160_length_108784_cov_106.859199 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.160 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141184 SAMEA13539216 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738610. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539216 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 16.4867 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_219_length_98000_cov_9.306373 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_219_length_98000_cov_9.306373 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.177 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141185 SAMEA13539217 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738610. BACPHLIP temperate score 0.16375920696193652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539217 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 10.7798 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_3246_length_19805_cov_5.886050 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; HMM-based (lower-bound) completeness score 61.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_3246_length_19805_cov_5.886050 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.3747 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141186 SAMEA13539218 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738610. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539218 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 20.058 MAG coverage software Reads (ERR7738610) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561162) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 54 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_5_1598__NODE_954_length_47773_cov_11.690624 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585847 sample name Hadza_MoBio_hadza-A-D_B_5_1598__NODE_954_length_47773_cov_11.690624 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738564_virus.149 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141187 SAMEA13539219 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738611. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539219 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 45.8447 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_171_length_166165_cov_28.512530_1 Viral contig found in MAG ERR7738611_bin.168 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_171_length_166165_cov_28.512530_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_virus.1424 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141188 SAMEA13539220 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738611. BACPHLIP temperate score 0.07403688597812165 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539220 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 29.6534 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2772_length_35597_cov_17.964414_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2772_length_35597_cov_17.964414_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745594_bin.6 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884;s__UBA5884 sp900551505 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_provirus.2772 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141189 SAMEA13539221 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738611. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539221 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 11.5891 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_402_length_110746_cov_7.027885_1 Viral contig found in MAG ERR7738611_bin.212 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_402_length_110746_cov_7.027885_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.212 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_provirus.402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141190 SAMEA13539222 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738611. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539222 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 14.8343 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 77 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_736_length_82516_cov_8.708221_1 Viral contig found in MAG ERR7738611_bin.182 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_736_length_82516_cov_8.708221_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738612_provirus.1138 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141191 SAMEA13539223 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539223 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 5.76918 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_11435_length_11839_cov_3.295188 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_11435_length_11839_cov_3.295188 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.262 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_virus.11435 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141192 SAMEA13539224 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0.375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539224 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 19.9449 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_149_length_178048_cov_11.988285 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 59.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_149_length_178048_cov_11.988285 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_virus.45 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141193 SAMEA13539225 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738611. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539225 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 45.1108 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 108 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_1899_length_46654_cov_27.044507 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_1899_length_46654_cov_27.044507 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738170_virus.283 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141194 SAMEA13539226 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539226 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 10.0204 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2315_length_40593_cov_6.054250 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2315_length_40593_cov_6.054250 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_virus.2315 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141195 SAMEA13539227 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539227 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 11.8539 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2538_length_37949_cov_7.127244 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3636363636363637 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2538_length_37949_cov_7.127244 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_virus.2538 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141196 SAMEA13539228 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539228 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 23.5696 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2672_length_36530_cov_13.967026 Viral contig found in MAG ERR7738611_bin.225 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_2672_length_36530_cov_13.967026 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_virus.2672 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141197 SAMEA13539229 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0.09759913048709812 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539229 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 21.5626 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_3025_length_33328_cov_13.352771 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_3025_length_33328_cov_13.352771 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.961 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141198 SAMEA13539230 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0.12951046580442682 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539230 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 21.0288 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_3423_length_30556_cov_12.714262 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_3423_length_30556_cov_12.714262 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746433_provirus.452 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141199 SAMEA13539231 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0.2599118942731277 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539231 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 7.49763 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_4956_length_23316_cov_4.386161 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_4956_length_23316_cov_4.386161 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738552_bin.355 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__CAG-238;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_virus.4956 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141200 SAMEA13539232 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539232 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 7.98969 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_5565_length_21396_cov_4.645574 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_5565_length_21396_cov_4.645574 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_provirus.1362 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141201 SAMEA13539233 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738611. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539233 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 57.9644 MAG coverage software Reads (ERR7738611) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559915) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-I-L_K_9_2483__NODE_886_length_73671_cov_34.963339 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6060606060606061 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586257 sample name Hadza_MoBio_hadza-I-L_K_9_2483__NODE_886_length_73671_cov_34.963339 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.790 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141202 SAMEA13539234 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738612. BACPHLIP temperate score 0.1751132947985236 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539234 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 85.497 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_158_length_154014_cov_48.862327_1 Viral contig found in MAG ERR7738612_bin.279 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_158_length_154014_cov_48.862327_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_provirus.24 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141203 SAMEA13539235 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738612. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539235 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 154.422 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_351_length_108015_cov_88.313967_1 Viral contig found in MAG ERR7738612_bin.111 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_351_length_108015_cov_88.313967_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738612_provirus.351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141204 SAMEA13539236 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738612. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539236 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 22.0452 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_704_length_76080_cov_12.439996_1 Viral contig found in MAG ERR7738612_bin.60 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_704_length_76080_cov_12.439996_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738231_virus.1408 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141205 SAMEA13539237 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738612. BACPHLIP temperate score 0.039370028578617 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539237 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 35.5234 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_1561_length_46805_cov_20.426596 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_1561_length_46805_cov_20.426596 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_provirus.996 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141206 SAMEA13539238 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738612. BACPHLIP temperate score 0.03978894729646896 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539238 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 39.307 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_1795_length_42974_cov_22.176143 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_1795_length_42974_cov_22.176143 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738170_provirus.992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141207 SAMEA13539239 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738612. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539239 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 16.9253 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_2233_length_36418_cov_9.532374 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; HMM-based (lower-bound) completeness score 75.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_2233_length_36418_cov_9.532374 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141208 SAMEA13539240 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738612. BACPHLIP temperate score 0.16464757709251104 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539240 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 114.955 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_2573_length_32286_cov_68.091434 Viral contig found in MAG ERR7738612_bin.111 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_2573_length_32286_cov_68.091434 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_provirus.1304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141209 SAMEA13539241 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738612. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539241 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 30.8186 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_413_length_100724_cov_17.525361 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 21 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.988095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_413_length_100724_cov_17.525361 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.372 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141210 SAMEA13539242 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738612. BACPHLIP temperate score 0.06078698503890495 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539242 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 99.0017 MAG coverage software Reads (ERR7738612) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559618) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-I-L_O_2_2674__NODE_8656_length_11212_cov_55.705344 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-21 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586372 sample name Hadza_MoBio_hadza-I-L_O_2_2674__NODE_8656_length_11212_cov_55.705344 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME181333 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900540885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738231_virus.7124 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11141211 SAMEA13539243 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738613. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539243 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:57Z INSDC last update 2022-12-27T00:30:57Z INSDC status public MAG coverage depth 89.0324 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1853_length_35877_cov_51.285922_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1853_length_35877_cov_51.285922_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME117056 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella sp002299315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.2092 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141212 SAMEA13539244 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738613. BACPHLIP temperate score 0.04171309743186609 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539244 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:58Z INSDC last update 2022-12-27T00:30:58Z INSDC status public MAG coverage depth 19.3928 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 109 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_404_length_84376_cov_11.386102_1 Viral contig found in MAG ERR7738613_bin.198 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_404_length_84376_cov_11.386102_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141213 SAMEA13539245 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738613. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539245 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 32.0183 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 222 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1059_length_49782_cov_19.250599 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1059_length_49782_cov_19.250599 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0339185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11141214 SAMEA13539246 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738613. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539246 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 13.7439 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1406_length_41963_cov_7.810223 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1406_length_41963_cov_7.810223 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.1406 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141215 SAMEA13539247 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738613. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539247 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 34.217 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1489_length_40573_cov_20.317834 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1489_length_40573_cov_20.317834 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.1099 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141216 SAMEA13539248 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738613. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539248 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 31.3465 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 213 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1679_length_38068_cov_24.812982 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1679_length_38068_cov_24.812982 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_provirus.383 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141217 SAMEA13539249 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus virus assembled from ERR7738613. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539249 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 13.2 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1924_length_34900_cov_7.582173 Viral contig found in MAG ERR7738613_bin.142 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_1924_length_34900_cov_7.582173 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738178_bin.23 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.1924 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11141218 SAMEA13539250 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7738613. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539250 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 6.56982 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_22389_length_5822_cov_3.788860 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_22389_length_5822_cov_3.788860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.15575 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11141219 SAMEA13539251 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738613. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539251 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 10.4145 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_282_length_100964_cov_5.738678 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6511627906976745 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_282_length_100964_cov_5.738678 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.282 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141220 SAMEA13539252 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738613. BACPHLIP temperate score 0.13705947136563884 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539252 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 8.52771 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_3518_length_23174_cov_4.776421 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_3518_length_23174_cov_4.776421 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.3518 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141221 SAMEA13539253 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738613. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539253 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 17.1487 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_4997_length_18359_cov_11.436221 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_4997_length_18359_cov_11.436221 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME086787 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C;s__Ruminococcus_C sp000433635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.4997 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141222 SAMEA13539254 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738613. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539254 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 23.1261 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_671_length_64090_cov_14.128068 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 77.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_671_length_64090_cov_14.128068 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.671 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141223 SAMEA13539255 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738613. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539255 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 72.5117 MAG coverage software Reads (ERR7738613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562068) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 141 Submitter Id Hadza_MoBio_hadza-E-H_G_9_1735__NODE_972_length_52725_cov_45.359843 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.43333333333333335 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585978 sample name Hadza_MoBio_hadza-E-H_G_9_1735__NODE_972_length_52725_cov_45.359843 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_provirus.872 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141224 SAMEA13539256 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738614. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539256 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:06Z INSDC last update 2022-12-27T00:31:06Z INSDC status public MAG coverage depth 66.6934 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_24_length_218357_cov_39.573122_1 Viral contig found in MAG ERR7738614_bin.69 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.380952380952381 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_24_length_218357_cov_39.573122_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_provirus.135 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141225 SAMEA13539257 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738614. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539257 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 49.6926 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_43_length_186647_cov_30.588026_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5111111111111111 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_43_length_186647_cov_30.588026_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME103816 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;s__Dorea_A longicatena vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_provirus.41 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141226 SAMEA13539258 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738614. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539258 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 18.4049 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_83_length_144955_cov_10.840611_1 Viral contig found in MAG ERR7738614_bin.112 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_83_length_144955_cov_10.840611_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738614_provirus.83 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141227 SAMEA13539259 2133760 Siphoviridae environmental samples This sample represents an uncultured Teubervirus virus assembled from ERR7738614. BACPHLIP temperate score 0.10658093884155775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539259 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 197.515 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_1322_length_34662_cov_119.973110 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_1322_length_34662_cov_119.973110 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Teubervirus virus enrichment approach none ERS11141228 SAMEA13539260 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738614. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539260 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 10.392 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_1655_length_29996_cov_6.185668 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_1655_length_29996_cov_6.185668 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001757 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella;s__Schaedlerella sp900066545 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738614_virus.1655 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141229 SAMEA13539261 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738614. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539261 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 14.0725 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_2447_length_23322_cov_8.131297 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_2447_length_23322_cov_8.131297 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME067489 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-217;s__CAG-217 sp000436335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_provirus.439 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141230 SAMEA13539262 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738614. BACPHLIP temperate score 0.15709857153129908 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539262 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 24.384 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_2927_length_20701_cov_14.791020 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_2927_length_20701_cov_14.791020 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME086861 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter;s__Fusicatenibacter saccharivorans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.2474 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141231 SAMEA13539263 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7738614. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539263 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 192.292 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_5705_length_13251_cov_115.477987 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_5705_length_13251_cov_115.477987 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.4087 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11141232 SAMEA13539264 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738614. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539264 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 37.3635 MAG coverage software Reads (ERR7738614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567908) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_863_length_44738_cov_22.848794 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585607 sample name Hadza_PheChl_Fiber-Hadza-Nepal_I_10_1184__NODE_863_length_44738_cov_22.848794 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.470 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11141233 SAMEA13539265 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738616. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539265 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 25.459 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1611_length_38550_cov_15.383360_1 Viral contig found in MAG ERR7738616_bin.84 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 57.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1611_length_38550_cov_15.383360_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746741_bin.80 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;s__RUG572 sp900547945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738141_provirus.71 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141234 SAMEA13539266 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738616. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539266 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 15.6023 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_56_length_204393_cov_9.319941_1 Viral contig found in MAG ERR7738616_bin.69 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_56_length_204393_cov_9.319941_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_virus.716 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141235 SAMEA13539267 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738616. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539267 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 15.9405 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_78_length_182516_cov_9.396242_1 Viral contig found in MAG ERR7738616_bin.66 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_78_length_182516_cov_9.396242_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_provirus.78 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141236 SAMEA13539268 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738616. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539268 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 16.6929 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1222_length_46503_cov_9.944428 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1222_length_46503_cov_9.944428 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_virus.1222 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141237 SAMEA13539269 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738616. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539269 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 9.50914 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1440_length_41867_cov_5.692845 Viral contig found in MAG ERR7738616_bin.26 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1440_length_41867_cov_5.692845 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746219_bin.253 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2883;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_virus.1440 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141238 SAMEA13539270 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738616. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539270 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 192.214 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 204 Number of CRISPR spacer hits supporting host taxonomy 124 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1769_length_36173_cov_146.703457 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_1769_length_36173_cov_146.703457 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_virus.1769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141239 SAMEA13539271 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738616. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539271 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 50.3738 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 256 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_2446_length_28480_cov_33.704503 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_2446_length_28480_cov_33.704503 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.2329 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141240 SAMEA13539272 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738616. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539272 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 79.1888 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 133 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_319_length_99633_cov_47.540078 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_319_length_99633_cov_47.540078 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141241 SAMEA13539273 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738616. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539273 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 55.2818 MAG coverage software Reads (ERR7738616) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559925) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-I-L_M_13_2496__NODE_521_length_78064_cov_32.425122 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586270 sample name Hadza_MoBio_hadza-I-L_M_13_2496__NODE_521_length_78064_cov_32.425122 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_virus.521 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141242 SAMEA13539274 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738617. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539274 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 276.704 MAG coverage software Reads (ERR7738617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 129 Submitter Id Hadza_MoBio_hadza-I-L_G_2_2602__NODE_111_length_148414_cov_169.333295_1 Viral contig found in MAG ERR7738617_bin.35 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.48484848484848486 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586313 sample name Hadza_MoBio_hadza-I-L_G_2_2602__NODE_111_length_148414_cov_169.333295_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738154_provirus.36 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141243 SAMEA13539275 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738617. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539275 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 37.3246 MAG coverage software Reads (ERR7738617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 80 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_G_2_2602__NODE_22_length_288334_cov_22.206569_1 Viral contig found in MAG ERR7738617_bin.90 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586313 sample name Hadza_MoBio_hadza-I-L_G_2_2602__NODE_22_length_288334_cov_22.206569_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738617_provirus.22 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141244 SAMEA13539276 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis provirus assembled from ERR7738617. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539276 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 12.7713 MAG coverage software Reads (ERR7738617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-I-L_G_2_2602__NODE_449_length_74767_cov_7.660021_1 Viral contig found in MAG ERR7738617_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5757575757575758 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586313 sample name Hadza_MoBio_hadza-I-L_G_2_2602__NODE_449_length_74767_cov_7.660021_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME007797 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__CAG-115 sp003531585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_provirus.44 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11141245 SAMEA13539277 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738617. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539277 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 10.44 MAG coverage software Reads (ERR7738617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-I-L_G_2_2602__NODE_93_length_163345_cov_5.958694_1 Viral contig found in MAG ERR7738617_bin.6 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6037735849056604 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586313 sample name Hadza_MoBio_hadza-I-L_G_2_2602__NODE_93_length_163345_cov_5.958694_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738617_provirus.93 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141246 SAMEA13539278 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738617. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539278 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 14.447 MAG coverage software Reads (ERR7738617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Hadza_MoBio_hadza-I-L_G_2_2602__NODE_1687_length_33539_cov_8.343763 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586313 sample name Hadza_MoBio_hadza-I-L_G_2_2602__NODE_1687_length_33539_cov_8.343763 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.999 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141247 SAMEA13539279 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738617. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539279 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 49.957 MAG coverage software Reads (ERR7738617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 137 Submitter Id Hadza_MoBio_hadza-I-L_G_2_2602__NODE_286_length_96398_cov_28.481037 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.380952380952381 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586313 sample name Hadza_MoBio_hadza-I-L_G_2_2602__NODE_286_length_96398_cov_28.481037 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738617_virus.286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141248 SAMEA13539280 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738617. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539280 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 32.1083 MAG coverage software Reads (ERR7738617) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559313) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-I-L_G_2_2602__NODE_668_length_61513_cov_18.649473 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586313 sample name Hadza_MoBio_hadza-I-L_G_2_2602__NODE_668_length_61513_cov_18.649473 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_virus.855 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141249 SAMEA13539281 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738619. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539281 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 237.189 MAG coverage software Reads (ERR7738619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568531) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_236_length_104010_cov_136.797966_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 50.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_236_length_104010_cov_136.797966_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745769_provirus.181 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141250 SAMEA13539282 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738619. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539282 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 19.4482 MAG coverage software Reads (ERR7738619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568531) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 232 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_536_length_65469_cov_11.089919_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8787878787878788 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_536_length_65469_cov_11.089919_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_C vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0379536 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141251 SAMEA13539283 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738619. BACPHLIP temperate score 0.13104347289138735 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539283 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 19.396 MAG coverage software Reads (ERR7738619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568531) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_921_length_44475_cov_10.866683_1 Viral contig found in MAG ERR7738619_bin.78 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_921_length_44475_cov_10.866683_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745769_provirus.441 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141252 SAMEA13539284 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738619. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539284 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:07Z INSDC last update 2022-12-27T00:31:07Z INSDC status public MAG coverage depth 7.74907 MAG coverage software Reads (ERR7738619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568531) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 460 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_1291_length_34119_cov_4.124581 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_1291_length_34119_cov_4.124581 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380247 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141253 SAMEA13539285 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738619. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539285 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 25.4495 MAG coverage software Reads (ERR7738619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568531) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_53_length_206038_cov_14.223518 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_53_length_206038_cov_14.223518 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738619_virus.53 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141254 SAMEA13539286 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738619. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539286 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 28.1877 MAG coverage software Reads (ERR7738619) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568531) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_983_length_42223_cov_15.799862 Viral contig found in MAG ERR7738619_bin.68 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6206896551724138 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_3_THA1067YZ_1__NODE_983_length_42223_cov_15.799862 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745769_virus.775 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141255 SAMEA13539287 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu provirus assembled from ERR7738620. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539287 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 13.4913 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_1703_length_47191_cov_7.655432_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.972972972972973 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_1703_length_47191_cov_7.655432_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738535_provirus.895 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11141256 SAMEA13539288 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738620. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539288 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 189.397 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 249 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_299_length_137573_cov_105.404295_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_299_length_137573_cov_105.404295_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738620_provirus.299 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141257 SAMEA13539289 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738620. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539289 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 14.0563 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 168 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_543_length_99106_cov_7.856204_1 Viral contig found in MAG ERR7738620_bin.89 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_543_length_99106_cov_7.856204_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001578 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__TF01-11 sp001414325 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738620_provirus.543 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141258 SAMEA13539290 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738620. BACPHLIP temperate score 0.65 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539290 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 19.6985 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_84_length_247936_cov_11.120419_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_84_length_247936_cov_11.120419_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME074354 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus;s__Negativibacillus sp000435195 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738620_provirus.84 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141259 SAMEA13539291 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738620. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539291 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 99.2184 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 273 Number of CRISPR spacer hits supporting host taxonomy 151 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_1384_length_55100_cov_55.109863 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6585365853658537 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_1384_length_55100_cov_55.109863 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.331 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141260 SAMEA13539292 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738620. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539292 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 39.1007 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 864 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_1629_length_48825_cov_22.155247 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_1629_length_48825_cov_22.155247 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0313669 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141261 SAMEA13539293 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738620. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539293 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 1520.3 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 430 Number of CRISPR spacer hits supporting host taxonomy 82 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_2052_length_40534_cov_850.182811 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_2052_length_40534_cov_850.182811 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0318076 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141262 SAMEA13539294 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738620. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539294 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 32.2206 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 215 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_2434_length_35118_cov_17.983391 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_2434_length_35118_cov_17.983391 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141263 SAMEA13539295 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738620. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539295 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 27.0653 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 456 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_2924_length_29834_cov_15.558457 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_2924_length_29834_cov_15.558457 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0305583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141264 SAMEA13539296 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738620. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13539296 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-28T19:46:14Z INSDC status public MAG coverage depth 100.208 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 514 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_3547_length_24667_cov_58.178528 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_3547_length_24667_cov_58.178528 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738549_virus.1198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141265 SAMEA13539297 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738620. BACPHLIP temperate score 0.19988986784140972 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539297 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 1234.54 MAG coverage software Reads (ERR7738620) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Pilot_MoBio_Fiber_C_24_1038__NODE_556_length_97955_cov_672.984981 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383817 sample name Pilot_MoBio_Fiber_C_24_1038__NODE_556_length_97955_cov_672.984981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147876 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides merdae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0378020 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141266 SAMEA13539298 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738621. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539298 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 12.696 MAG coverage software Reads (ERR7738621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567230) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_230_length_128898_cov_7.351790_1 Viral contig found in MAG ERR7738621_bin.157 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6904761904761905 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787376 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_230_length_128898_cov_7.351790_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0360932 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141267 SAMEA13539299 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738621. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539299 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 62.1698 MAG coverage software Reads (ERR7738621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567230) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 71 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_585_length_73191_cov_40.650573_1 Viral contig found in MAG ERR7738621_bin.200 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787376 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_585_length_73191_cov_40.650573_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_provirus.585 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141268 SAMEA13539300 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738621. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539300 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 26.0386 MAG coverage software Reads (ERR7738621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567230) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 79 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_1295_length_43320_cov_15.811761 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787376 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_1295_length_43320_cov_15.811761 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.1295 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141269 SAMEA13539301 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738621. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539301 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:18Z INSDC last update 2022-12-27T00:31:18Z INSDC status public MAG coverage depth 13.7713 MAG coverage software Reads (ERR7738621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567230) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 61 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_1577_length_37354_cov_8.329238 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787376 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_1577_length_37354_cov_8.329238 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738144_virus.294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141270 SAMEA13539302 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738621. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539302 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 27.9801 MAG coverage software Reads (ERR7738621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567230) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_1780_length_34052_cov_16.833966 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787376 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_1780_length_34052_cov_16.833966 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME015136 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;s__Oribacterium sp004554245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.1780 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141271 SAMEA13539303 336724 Myoviridae environmental samples This sample represents an uncultured Klebsiella phage vB_Kpn_Chronis virus assembled from ERR7738621. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539303 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 9.97818 MAG coverage software Reads (ERR7738621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567230) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1113 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_2352_length_26910_cov_5.736034 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8214285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787376 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_2352_length_26910_cov_5.736034 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738619_provirus.722 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Klebsiella phage vB_Kpn_Chronis virus enrichment approach none ERS11141272 SAMEA13539304 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738621. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539304 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 31.9603 MAG coverage software Reads (ERR7738621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567230) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_669_length_66994_cov_19.289104 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787376 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_17_RAJ0019YZ__NODE_669_length_66994_cov_19.289104 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0344814 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141273 SAMEA13539305 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738622. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539305 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 23.6872 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1080_length_66357_cov_13.600347_1 Viral contig found in MAG ERR7738622_bin.29 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.90625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1080_length_66357_cov_13.600347_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.2214 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141274 SAMEA13539306 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738622. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539306 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 14.6619 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1555_length_51925_cov_8.215939_1 Viral contig found in MAG ERR7738622_bin.4 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1555_length_51925_cov_8.215939_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.1328 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141275 SAMEA13539307 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738622. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539307 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 58.6343 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 117 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2675_length_35947_cov_33.724589_1 Viral contig found in MAG ERR7738622_bin.342 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2675_length_35947_cov_33.724589_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737966_provirus.195 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141276 SAMEA13539308 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738622. BACPHLIP temperate score 0.16636888074277426 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539308 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 673.618 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 53 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_531_length_100010_cov_430.630983_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_531_length_100010_cov_430.630983_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.895 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141277 SAMEA13539309 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539309 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 31.7818 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_107_length_203772_cov_17.602474 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 95.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6515151515151515 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_107_length_203772_cov_17.602474 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.93 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820;s__UMGS1820 sp900545865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.80 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141278 SAMEA13539310 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738622. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539310 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 30.8313 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1289_length_58946_cov_18.125720 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1289_length_58946_cov_18.125720 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141279 SAMEA13539311 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539311 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 72.8618 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1452_length_54205_cov_40.573215 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7058823529411765 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1452_length_54205_cov_40.573215 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp003514385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.589 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141280 SAMEA13539312 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738622. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539312 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 20.5825 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1630_length_50489_cov_11.244723 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_1630_length_50489_cov_11.244723 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745419_virus.909 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141281 SAMEA13539313 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738622. BACPHLIP temperate score 0.3974118942731278 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539313 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 104.656 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_181_length_170056_cov_59.059454 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 20 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.5370370370370371 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_181_length_170056_cov_59.059454 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.140 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141282 SAMEA13539314 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738622. BACPHLIP temperate score 0.0758246448305204 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539314 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 15.39 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_197_length_161909_cov_8.488482 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_197_length_161909_cov_8.488482 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.197 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141283 SAMEA13539315 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.3875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539315 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 99.0921 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2096_length_42386_cov_70.276915 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2096_length_42386_cov_70.276915 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME172369 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-917;g__CAG-349;s__CAG-349 sp003539515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1869 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141284 SAMEA13539316 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539316 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 22.7921 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2331_length_39488_cov_12.559742 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2331_length_39488_cov_12.559742 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.2331 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141285 SAMEA13539317 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.0292130974318661 ENA-FIRST-PUBLIC 2022-12-27T00:31:19Z ENA-LAST-UPDATE 2022-12-27T00:31:19Z External Id SAMEA13539317 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 11.1 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2522_length_37323_cov_6.286098 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2522_length_37323_cov_6.286098 scientific_name Siphoviridae environmental samples sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae ERS11141286 SAMEA13539318 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539318 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 80.0666 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2674_length_35949_cov_45.513242 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_2674_length_35949_cov_45.513242 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0281755 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141287 SAMEA13539319 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539319 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 64.2808 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_286_length_137918_cov_35.654841 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_286_length_137918_cov_35.654841 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.249 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141288 SAMEA13539320 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539320 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 75.484 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_326_length_131687_cov_41.669455 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 23 number of unique standard tRNAs extracted 18 percent of BLAST hits supporting viral taxonomy 0.5692307692307692 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_326_length_131687_cov_41.669455 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738227_provirus.7 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141289 SAMEA13539321 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539321 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 18.4228 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_3654_length_28589_cov_10.222257 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_3654_length_28589_cov_10.222257 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.3335 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141290 SAMEA13539322 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.675 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539322 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:31:19Z INSDC last update 2022-12-27T00:31:19Z INSDC status public MAG coverage depth 85.1302 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_4321_length_25038_cov_47.794840 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_4321_length_25038_cov_47.794840 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1228 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141291 SAMEA13539323 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.11754819338193057 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539323 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 15.0809 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_4967_length_22309_cov_8.896815 Viral contig found in MAG ERR7738622_bin.230 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_4967_length_22309_cov_8.896815 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124681 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__CAG-115 sp000432175 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.4967 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141292 SAMEA13539324 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7738622. BACPHLIP temperate score 0.2445250585754259 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539324 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:15Z INSDC last update 2022-12-27T00:30:15Z INSDC status public MAG coverage depth 37.5645 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_561_length_96509_cov_20.716142 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.971830985915493 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_561_length_96509_cov_20.716142 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.389 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11141293 SAMEA13539325 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539325 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 18.7011 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_7390_length_16180_cov_10.428988 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_7390_length_16180_cov_10.428988 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_virus.7390 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141294 SAMEA13539326 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738622. BACPHLIP temperate score 0.07634348183251045 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539326 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 8.16592 MAG coverage software Reads (ERR7738622) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561693) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_F_8_1202__NODE_926_length_72462_cov_4.402722 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.4705882352941176 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585625 sample name Hadza_MoBio_hadza-I-L_F_8_1202__NODE_926_length_72462_cov_4.402722 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.209 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141295 SAMEA13539327 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738623. BACPHLIP temperate score 0.05236784140969162 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539327 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 24.6587 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_1328_length_64368_cov_14.732684_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_1328_length_64368_cov_14.732684_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_provirus.1328 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141296 SAMEA13539328 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738623. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539328 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 177.474 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_19_length_407728_cov_130.914125_1 Viral contig found in MAG ERR7738623_bin.155 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_19_length_407728_cov_130.914125_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141297 SAMEA13539329 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738623. BACPHLIP temperate score 0.03469162995594714 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539329 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 25.4774 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2941_length_38609_cov_13.940828_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2941_length_38609_cov_13.940828_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.2135 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141298 SAMEA13539330 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738623. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539330 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 13.5467 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_5405_length_23888_cov_7.682290_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_5405_length_23888_cov_7.682290_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME280504 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900555735 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_virus.927 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141299 SAMEA13539331 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738623. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539331 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 9.06782 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_960_length_78533_cov_4.805968_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_960_length_78533_cov_4.805968_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_provirus.960 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141300 SAMEA13539332 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539332 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 29.6437 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_1453_length_61277_cov_16.002958 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_1453_length_61277_cov_16.002958 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.1453 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141301 SAMEA13539333 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539333 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 56.6677 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2006_length_50140_cov_31.044324 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2006_length_50140_cov_31.044324 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.2006 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141302 SAMEA13539334 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539334 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 98.6439 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2271_length_46600_cov_54.400662 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2271_length_46600_cov_54.400662 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.2271 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141303 SAMEA13539335 2133760 Siphoviridae environmental samples This sample represents an uncultured unclassified Kagunavirus virus assembled from ERR7738623. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539335 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 88.0282 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2443_length_44423_cov_47.904839 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.647887323943662 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2443_length_44423_cov_47.904839 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.2443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Guernseyvirinae; Kagunavirus; unclassified Kagunavirus virus enrichment approach none ERS11141304 SAMEA13539336 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7738623. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539336 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 55.7556 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 744 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2601_length_42352_cov_31.433235 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6129032258064516 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2601_length_42352_cov_31.433235 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.2601 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141305 SAMEA13539337 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539337 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 17.5866 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2754_length_40490_cov_9.588004 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_2754_length_40490_cov_9.588004 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.2754 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141306 SAMEA13539338 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.1380538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539338 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 37.9364 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 62 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3027_length_37764_cov_22.492106 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3027_length_37764_cov_22.492106 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738249_virus.786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141307 SAMEA13539339 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539339 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 24.0657 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3123_length_36931_cov_13.318527 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3123_length_36931_cov_13.318527 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_virus.1199 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141308 SAMEA13539340 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539340 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 22.1891 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3330_length_35302_cov_12.905323 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3330_length_35302_cov_12.905323 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.3330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141309 SAMEA13539341 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539341 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 11.9344 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3607_length_33040_cov_6.476049 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_3607_length_33040_cov_6.476049 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.3607 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141310 SAMEA13539342 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539342 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 25.8844 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_4328_length_28540_cov_14.720655 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_4328_length_28540_cov_14.720655 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.4328 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141311 SAMEA13539343 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738623. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539343 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 299.354 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_545_length_109168_cov_181.391911 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9583333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_545_length_109168_cov_181.391911 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738616_bin.92 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745398_virus.207 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141312 SAMEA13539344 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738623. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539344 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 24.1145 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_6621_length_20025_cov_14.348606 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_6621_length_20025_cov_14.348606 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.6964 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141313 SAMEA13539345 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738623. BACPHLIP temperate score 0.0490368859781216 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539345 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 120.14 MAG coverage software Reads (ERR7738623) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560388) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_13_1776__NODE_9006_length_15431_cov_65.908628 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585998 sample name Hadza_MoBio_hadza-E-H_K_13_1776__NODE_9006_length_15431_cov_65.908628 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.9006 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141314 SAMEA13539346 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738624. BACPHLIP temperate score 0.939977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539346 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 77.7798 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1360_length_69077_cov_42.582609_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 78.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3636363636363637 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1360_length_69077_cov_42.582609_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746349_bin.268 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA5920;s__UBA5920 sp002406055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_provirus.1360 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141315 SAMEA13539347 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738624. BACPHLIP temperate score 0.7243672824538925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539347 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 80.0368 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 108 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2071_length_51432_cov_44.450609_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2071_length_51432_cov_44.450609_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_virus.1910 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141316 SAMEA13539348 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738624. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539348 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 11.8076 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3315_length_37000_cov_6.339355_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3315_length_37000_cov_6.339355_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.430 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141317 SAMEA13539349 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738624. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539349 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 25.724 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 76 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_82_length_307987_cov_14.584418_1 Viral contig found in MAG ERR7738624_bin.254 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_82_length_307987_cov_14.584418_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME087442 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger sp900540775 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_provirus.82 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141318 SAMEA13539350 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539350 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 18.5762 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1121_length_77827_cov_10.263434 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; HMM-based (lower-bound) completeness score 94.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1121_length_77827_cov_10.263434 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.1121 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141319 SAMEA13539351 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539351 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 49.2592 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1604_length_62260_cov_26.977084 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1604_length_62260_cov_26.977084 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141320 SAMEA13539352 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.14693597737148006 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539352 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 9.13522 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_17409_length_8995_cov_5.005831 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_17409_length_8995_cov_5.005831 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738240_virus.6136 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141321 SAMEA13539353 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.06497797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539353 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 145.268 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 60 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1936_length_53914_cov_79.535877 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.675 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_1936_length_53914_cov_79.535877 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.1936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141322 SAMEA13539354 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738624. BACPHLIP temperate score 0.03576461450908247 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539354 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 6.27637 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_22395_length_7061_cov_3.252005 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_22395_length_7061_cov_3.252005 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738664_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.22395 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141323 SAMEA13539355 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.65 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539355 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 11.5687 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 266 Number of CRISPR spacer hits supporting host taxonomy 211 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2414_length_46217_cov_6.203229 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2414_length_46217_cov_6.203229 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0354261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141324 SAMEA13539356 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539356 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 25.5991 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2662_length_43050_cov_14.888767 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2662_length_43050_cov_14.888767 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.2662 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141325 SAMEA13539357 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539357 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 90.3341 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2790_length_41636_cov_49.421449 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2790_length_41636_cov_49.421449 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.2790 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141326 SAMEA13539358 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.2123898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539358 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 173.999 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 264 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2888_length_40667_cov_96.042868 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_2888_length_40667_cov_96.042868 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141327 SAMEA13539359 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539359 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 12.5313 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3043_length_39255_cov_6.667492 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3043_length_39255_cov_6.667492 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.328 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1750;g__UBA7102;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.3043 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141328 SAMEA13539360 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539360 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:16Z INSDC last update 2022-12-27T00:30:16Z INSDC status public MAG coverage depth 9.73335 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 93 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3414_length_36441_cov_5.270047 Viral contig found in MAG ERR7738624_bin.79 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3414_length_36441_cov_5.270047 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_provirus.1694 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141329 SAMEA13539361 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539361 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 93.2575 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 70 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3596_length_35131_cov_57.202630 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_3596_length_35131_cov_57.202630 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.3596 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141330 SAMEA13539362 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539362 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 96.3481 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 99 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_4017_length_32463_cov_101.704718 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8214285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_4017_length_32463_cov_101.704718 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.4017 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141331 SAMEA13539363 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539363 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 53.8785 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_4353_length_30404_cov_30.082105 Viral contig found in MAG ERR7738624_bin.169 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_4353_length_30404_cov_30.082105 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__UBA1234;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.4353 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141332 SAMEA13539364 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539364 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 29.5677 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_524_length_120294_cov_16.247103 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 12 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.6779661016949152 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_524_length_120294_cov_16.247103 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746738_bin.136 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900554275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141333 SAMEA13539365 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539365 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 229.786 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 162 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_6249_length_22533_cov_125.240871 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_6249_length_22533_cov_125.240871 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.6249 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141334 SAMEA13539366 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738624. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539366 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 15.4215 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_692_length_101877_cov_8.391022 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8409090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_692_length_101877_cov_8.391022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.692 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141335 SAMEA13539367 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7738624. BACPHLIP temperate score 0.13923512386358416 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539367 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 13.1483 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 136 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_8489_length_17364_cov_6.924625 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_8489_length_17364_cov_6.924625 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738221_virus.847 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11141336 SAMEA13539368 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738624. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539368 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 10.1846 MAG coverage software Reads (ERR7738624) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561717) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_F_16_1210__NODE_9966_length_15123_cov_5.929483 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585633 sample name Hadza_MoBio_hadza-I-L_F_16_1210__NODE_9966_length_15123_cov_5.929483 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME129025 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp900763685 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.9966 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141337 SAMEA13539369 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738626. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539369 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 174.501 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_143_length_187871_cov_98.686545_1 Viral contig found in MAG ERR7738626_bin.497 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_143_length_187871_cov_98.686545_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_provirus.272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141338 SAMEA13539370 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738626. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539370 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 35.0927 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2664_length_44145_cov_19.909345_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2664_length_44145_cov_19.909345_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_provirus.2664 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141339 SAMEA13539371 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738626. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539371 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 70.6164 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_525_length_116744_cov_39.395356_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_525_length_116744_cov_39.395356_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME233192 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus ruminis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_provirus.525 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141340 SAMEA13539372 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738626. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539372 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 15.8897 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_765_length_96270_cov_9.603984_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_765_length_96270_cov_9.603984_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_provirus.765 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141341 SAMEA13539373 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539373 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:11Z INSDC last update 2022-12-27T19:09:11Z INSDC status public MAG coverage depth 47.6875 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_102_length_211674_cov_30.849743 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 25 number of unique standard tRNAs extracted 18 percent of BLAST hits supporting viral taxonomy 0.676056338028169 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_102_length_211674_cov_30.849743 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.102 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141342 SAMEA13539374 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539374 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 215.298 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1110_length_77006_cov_126.939711 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6486486486486487 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1110_length_77006_cov_126.939711 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738148_bin.20 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A;s__Selenomonas_A sp900769615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.1110 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141343 SAMEA13539375 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738626. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539375 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:20Z INSDC last update 2022-12-27T00:30:20Z INSDC status public MAG coverage depth 150.764 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1342_length_68258_cov_85.979569 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1342_length_68258_cov_85.979569 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745545_provirus.108 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141344 SAMEA13539376 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738626. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539376 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 14.9465 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1574_length_61762_cov_8.956294 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9594594594594594 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1574_length_61762_cov_8.956294 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.1574 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141345 SAMEA13539377 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738626. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539377 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 51.7565 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1790_length_57244_cov_30.389333 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_1790_length_57244_cov_30.389333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.1790 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141346 SAMEA13539378 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7738626. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539378 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 36.8579 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 211 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2055_length_52449_cov_22.220404 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48484848484848486 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2055_length_52449_cov_22.220404 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024263 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides sp900549585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0328206 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11141347 SAMEA13539379 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738626. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539379 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 18.6735 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_217_length_162704_cov_11.091166 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.711864406779661 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_217_length_162704_cov_11.091166 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME007974 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp003516765 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.217 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141348 SAMEA13539380 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539380 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 45.6976 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 138 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2415_length_47166_cov_27.405211 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 70.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2415_length_47166_cov_27.405211 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.2415 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141349 SAMEA13539381 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539381 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 21.1581 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2704_length_43563_cov_11.869958 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_2704_length_43563_cov_11.869958 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.2704 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141350 SAMEA13539382 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539382 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 17.5604 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_282_length_148810_cov_10.559761 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6101694915254238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_282_length_148810_cov_10.559761 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746285_bin.102 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFTH01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.164 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141351 SAMEA13539383 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539383 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 22.9283 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3011_length_40155_cov_13.094316 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3011_length_40155_cov_13.094316 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_virus.1078 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141352 SAMEA13539384 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539384 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 13.2549 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3219_length_38352_cov_7.504376 Viral contig found in MAG ERR7738626_bin.294 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3219_length_38352_cov_7.504376 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.3219 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141353 SAMEA13539385 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539385 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 7.14563 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3319_length_37497_cov_4.130786 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3319_length_37497_cov_4.130786 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738264_bin.256 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__UBA4644;s__UBA4644 sp900763355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.3319 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141354 SAMEA13539386 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738626. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539386 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 104.277 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3597_length_35552_cov_62.133559 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42105263157894735 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3597_length_35552_cov_62.133559 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.3597 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141355 SAMEA13539387 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539387 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 80.6969 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3880_length_33552_cov_48.034503 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3880_length_33552_cov_48.034503 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.3880 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141356 SAMEA13539388 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.04616727037876595 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539388 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 95.5699 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 124 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3964_length_33012_cov_53.950235 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_3964_length_33012_cov_53.950235 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.3964 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141357 SAMEA13539389 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539389 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 38.1568 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_4360_length_30740_cov_22.127907 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_4360_length_30740_cov_22.127907 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746742_provirus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141358 SAMEA13539390 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738626. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539390 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 15.9107 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_5141_length_26778_cov_9.826561 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_5141_length_26778_cov_9.826561 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.5141 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141359 SAMEA13539391 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.17820990407225873 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539391 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 842.724 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_5530_length_25352_cov_517.558932 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_5530_length_25352_cov_517.558932 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.5530 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141360 SAMEA13539392 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738626. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539392 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 15.194 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_5924_length_24056_cov_10.774344 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_5924_length_24056_cov_10.774344 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.1659 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141361 SAMEA13539393 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738626. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539393 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 16.1415 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 846 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_674_length_103208_cov_9.390940 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3703703703703703 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_674_length_103208_cov_9.390940 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0368347 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141362 SAMEA13539394 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738626. BACPHLIP temperate score 0.6875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539394 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 15.0091 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_71_length_231910_cov_9.018556 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_71_length_231910_cov_9.018556 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME246739 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;s__Lachnospira eligens_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.71 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141364 SAMEA13539396 336724 Myoviridae environmental samples This sample represents an uncultured Acinetobacter phage MD-2021a virus assembled from ERR7738626. BACPHLIP temperate score 0.09666904456843 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539396 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 9.4229 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_833_length_91666_cov_5.328850 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_833_length_91666_cov_5.328850 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738582_bin.61 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA1829;s__UBA1829 sp900549415 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0378462 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Acinetobacter phage MD-2021a virus enrichment approach none ERS11141365 SAMEA13539397 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738627. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539397 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 12.752 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 114 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_1066_length_53616_cov_6.996227_1 Viral contig found in MAG ERR7738627_bin.86 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_1066_length_53616_cov_6.996227_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.2506 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141366 SAMEA13539398 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738627. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539398 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 35.8294 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_18_length_314921_cov_20.325888_1 Viral contig found in MAG ERR7738627_bin.181 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_18_length_314921_cov_20.325888_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME103816 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;s__Dorea_A longicatena vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738627_provirus.18 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141367 SAMEA13539399 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738627. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539399 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 9.98993 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 866 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_287_length_112226_cov_5.428332_1 Viral contig found in MAG ERR7738627_bin.79 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_287_length_112226_cov_5.428332_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001734 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides uniformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0297872 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141368 SAMEA13539400 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738627. BACPHLIP temperate score 0.6694113353173287 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539400 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 433.021 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 749 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_787_length_64860_cov_243.055292_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8620689655172413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_787_length_64860_cov_243.055292_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.235 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141369 SAMEA13539401 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738627. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539401 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 107.142 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_122_length_165359_cov_59.554265 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 97.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4358974358974359 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_122_length_165359_cov_59.554265 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0377424 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141370 SAMEA13539402 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738627. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539402 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 103.532 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_161_length_145778_cov_56.659172 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.6290322580645161 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_161_length_145778_cov_56.659172 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_virus.64 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141371 SAMEA13539403 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738627. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539403 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 11.8881 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 88 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_1934_length_35085_cov_6.597892 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6551724137931034 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_1934_length_35085_cov_6.597892 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_provirus.1146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141372 SAMEA13539404 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738627. BACPHLIP temperate score 0.11854347289138734 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539404 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 14.9558 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_211_length_129774_cov_8.142178 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.5675675675675675 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_211_length_129774_cov_8.142178 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738627_virus.211 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141373 SAMEA13539405 2133760 Siphoviridae environmental samples This sample represents an uncultured Erysipelothrix phage phi1605 virus assembled from ERR7738627. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539405 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 232.115 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_3336_length_21738_cov_130.460228 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_3336_length_21738_cov_130.460228 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737969_virus.1469 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Erysipelothrix phage phi1605 virus enrichment approach none ERS11141374 SAMEA13539406 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738627. BACPHLIP temperate score 0.08491189427312776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539406 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 17.63 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_3998_length_18291_cov_9.886516 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_3998_length_18291_cov_9.886516 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738627_virus.3998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141375 SAMEA13539407 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738627. BACPHLIP temperate score 0.7773678414096915 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539407 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 35.5911 MAG coverage software Reads (ERR7738627) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561880) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_6_1150__NODE_775_length_65283_cov_19.846026 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585574 sample name Hadza_MoBio_hadza-A-D_K_6_1150__NODE_775_length_65283_cov_19.846026 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.456 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141376 SAMEA13539408 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738628. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539408 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 34.5674 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_10_length_430606_cov_20.313324_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 16 number of unique standard tRNAs extracted 12 percent of BLAST hits supporting viral taxonomy 0.603448275862069 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_10_length_430606_cov_20.313324_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_virus.76 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141377 SAMEA13539409 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738628. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539409 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 11.8742 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_125_length_197494_cov_7.145874_1 Viral contig found in MAG ERR7738628_bin.251 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_125_length_197494_cov_7.145874_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196;s__CAG-196 sp900553895 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738174_provirus.59 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141378 SAMEA13539410 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738628. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539410 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 11.8686 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_1557_length_52925_cov_6.912561_1 Viral contig found in MAG ERR7738628_bin.38 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_1557_length_52925_cov_6.912561_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS902;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.1557 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141379 SAMEA13539411 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738628. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539411 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 18.9758 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_1991_length_45489_cov_11.016758_1 Viral contig found in MAG ERR7738628_bin.459 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_1991_length_45489_cov_11.016758_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_provirus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141380 SAMEA13539412 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738628. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539412 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 106.69 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2577_length_38727_cov_61.143984_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2577_length_38727_cov_61.143984_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.2577 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141381 SAMEA13539413 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738628. BACPHLIP temperate score 0.1574339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539413 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 46.8744 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3489_length_32501_cov_29.901709_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9583333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3489_length_32501_cov_29.901709_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.3489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141382 SAMEA13539414 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738628. BACPHLIP temperate score 0.20743392070484584 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539414 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 10.418 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_634_length_86014_cov_5.625784_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_634_length_86014_cov_5.625784_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.2031 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141383 SAMEA13539415 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738628. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539415 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 291.826 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 145 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_956_length_70063_cov_172.460978_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 61.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_956_length_70063_cov_172.460978_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141384 SAMEA13539416 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539416 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 38.9569 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_11190_length_14529_cov_22.237130 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_11190_length_14529_cov_22.237130 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000426 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A sp900066205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.8840 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11141385 SAMEA13539417 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539417 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 17.6161 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_1398_length_56395_cov_10.232608 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_1398_length_56395_cov_10.232608 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.1369 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141386 SAMEA13539419 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539419 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 7.94501 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_18628_length_9789_cov_4.471890 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_18628_length_9789_cov_4.471890 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.11552 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11141387 SAMEA13539420 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539420 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 13.8899 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 106 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2247_length_42103_cov_7.861134 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8484848484848485 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2247_length_42103_cov_7.861134 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.945 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141388 SAMEA13539421 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539421 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 11.8422 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2444_length_40069_cov_6.731396 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2444_length_40069_cov_6.731396 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_provirus.273 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141389 SAMEA13539422 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539422 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 11.0627 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2829_length_36723_cov_6.448071 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_2829_length_36723_cov_6.448071 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.1657 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141390 SAMEA13539423 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7738628. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539423 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:24Z INSDC last update 2022-12-27T00:30:24Z INSDC status public MAG coverage depth 15.6658 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3125_length_34673_cov_9.159932 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9310344827586208 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3125_length_34673_cov_9.159932 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_provirus.213 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141391 SAMEA13539424 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 4.9472295514511e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539424 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 18.028 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3382_length_33089_cov_10.512935 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3382_length_33089_cov_10.512935 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096004 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__Desulfovibrio piger vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.1884 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141392 SAMEA13539425 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539425 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 28.2721 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 138 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3981_length_29803_cov_17.359012 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_3981_length_29803_cov_17.359012 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.3981 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141393 SAMEA13539426 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539426 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 25.1648 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_4470_length_27745_cov_14.512289 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_4470_length_27745_cov_14.512289 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.4103 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141394 SAMEA13539427 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.02673512386358416 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539427 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 99.8483 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_5769_length_23200_cov_57.775072 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_5769_length_23200_cov_57.775072 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.220 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141395 SAMEA13539428 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.05927917672702029 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539428 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 11.8221 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_6656_length_20994_cov_7.065162 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_6656_length_20994_cov_7.065162 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745854_bin.180 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.4620 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141396 SAMEA13539429 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738628. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539429 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 16.9451 MAG coverage software Reads (ERR7738628) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567910) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_8397_length_17902_cov_9.833885 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585884 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_14_1640__NODE_8397_length_17902_cov_9.833885 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME017973 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__UMGS124;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.8397 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141397 SAMEA13539430 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738629. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539430 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 47.7627 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_147_length_136264_cov_27.971121_1 Viral contig found in MAG ERR7738629_bin.140 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_147_length_136264_cov_27.971121_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_provirus.800 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141398 SAMEA13539431 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7738629. BACPHLIP temperate score 0.27241189427312773 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539431 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 15.5066 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_343_length_92715_cov_8.955170_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_343_length_92715_cov_8.955170_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_provirus.343 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141399 SAMEA13539432 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738629. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539432 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 29.7565 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 83 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_542_length_72053_cov_17.514157_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9107142857142856 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_542_length_72053_cov_17.514157_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738256_virus.400 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141400 SAMEA13539433 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738629. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539433 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 335.263 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 130 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_877_length_55204_cov_225.212527_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_877_length_55204_cov_225.212527_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141401 SAMEA13539434 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738629. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539434 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 165.243 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_1222_length_44361_cov_97.015559 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_1222_length_44361_cov_97.015559 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.227 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141402 SAMEA13539435 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738629. BACPHLIP temperate score 0.09245594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539435 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 12.3997 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_1616_length_36913_cov_6.978255 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.935483870967742 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_1616_length_36913_cov_6.978255 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141403 SAMEA13539436 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738629. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539436 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 10.0373 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_2236_length_29532_cov_5.709217 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_2236_length_29532_cov_5.709217 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738588_bin.89 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_virus.2236 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141404 SAMEA13539437 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738629. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539437 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:25Z INSDC last update 2022-12-27T00:30:25Z INSDC status public MAG coverage depth 10.2721 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 77 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_2693_length_25529_cov_5.664545 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_2693_length_25529_cov_5.664545 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_virus.2693 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141405 SAMEA13539438 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738629. BACPHLIP temperate score 0.1940058974551755 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539438 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 395.893 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 198 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_3241_length_22147_cov_346.848890 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_3241_length_22147_cov_346.848890 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_provirus.918 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141406 SAMEA13539439 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738629. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539439 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 29.7677 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_661_length_64588_cov_17.269504 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_661_length_64588_cov_17.269504 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738566_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.541 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141407 SAMEA13539440 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7738629. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539440 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 10.9573 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_843_length_56559_cov_6.415902 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9423076923076924 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_843_length_56559_cov_6.415902 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0338867 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141408 SAMEA13539441 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738629. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539441 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 22.3057 MAG coverage software Reads (ERR7738629) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561301) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 79 Submitter Id Hadza_MoBio_hadza-I-L_N_17_1305__NODE_94_length_159386_cov_13.265798 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7377049180327869 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585720 sample name Hadza_MoBio_hadza-I-L_N_17_1305__NODE_94_length_159386_cov_13.265798 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738605_virus.100 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141409 SAMEA13539442 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738630. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539442 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 26.5067 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1469_length_60587_cov_15.630689_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1469_length_60587_cov_15.630689_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.1126 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141410 SAMEA13539443 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738630. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539443 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 26.0074 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 96 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_208_length_192523_cov_14.741257_1 Viral contig found in MAG ERR7738630_bin.180 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_208_length_192523_cov_14.741257_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-313;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_provirus.208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141411 SAMEA13539444 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738630. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539444 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 53.2159 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_383_length_138006_cov_29.148982_1 Viral contig found in MAG ERR7738630_bin.202 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_383_length_138006_cov_29.148982_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_provirus.383 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141412 SAMEA13539445 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738630. BACPHLIP temperate score 0.3875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539445 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 209.04 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_888_length_84185_cov_118.308853_1 Viral contig found in MAG ERR7738630_bin.226 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_888_length_84185_cov_118.308853_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746757_provirus.29 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141413 SAMEA13539446 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738630. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539446 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 45.3585 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1328_length_64808_cov_25.458714 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9318181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1328_length_64808_cov_25.458714 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.1328 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141414 SAMEA13539447 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738630. BACPHLIP temperate score 0.07804291393558824 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539447 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 64.3413 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1552_length_58037_cov_35.339545 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1552_length_58037_cov_35.339545 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.1552 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141415 SAMEA13539448 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7738630. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539448 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 78.7506 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 595 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1871_length_50711_cov_43.484141 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8032786885245902 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_1871_length_50711_cov_43.484141 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11141416 SAMEA13539449 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738630. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539449 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 10.7964 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2205_length_44977_cov_5.840935 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2205_length_44977_cov_5.840935 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738568_bin.326 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__SFEL01;s__SFEL01 sp004557245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_provirus.614 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141417 SAMEA13539450 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738630. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539450 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 45.2111 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 484 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2305_length_43708_cov_28.568334 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.4827586206896552 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2305_length_43708_cov_28.568334 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738242_virus.549 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141418 SAMEA13539451 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738630. BACPHLIP temperate score 0.06384348183251046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539451 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 411.23 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2411_length_42214_cov_226.859316 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2411_length_42214_cov_226.859316 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745890_bin.206 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.2411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141419 SAMEA13539452 1478972 Gokushovirinae environmental samples This sample represents an uncultured Chlamydiamicrovirus virus assembled from ERR7738630. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539452 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 8.64988 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_25696_length_5334_cov_4.545939 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_25696_length_5334_cov_4.545939 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738513_bin.39 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag1;s__Zag1 sp001765415 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.25696 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; Chlamydiamicrovirus virus enrichment approach none ERS11141420 SAMEA13539453 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738630. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539453 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 10.1063 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2725_length_38483_cov_5.465474 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2725_length_38483_cov_5.465474 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.2601 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141421 SAMEA13539454 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738630. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539454 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 99.7514 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2963_length_36167_cov_55.489609 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_2963_length_36167_cov_55.489609 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.2963 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141422 SAMEA13539455 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738630. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539455 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 61.2136 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_3264_length_33299_cov_49.897538 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_3264_length_33299_cov_49.897538 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.3264 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141423 SAMEA13539456 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738630. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539456 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 9.06166 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 70 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_3840_length_29149_cov_5.175117 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_3840_length_29149_cov_5.175117 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.994 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141424 SAMEA13539457 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7738630. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539457 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 3.92001 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_44605_length_3238_cov_1.879152 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_44605_length_3238_cov_1.879152 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.44605 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11141425 SAMEA13539458 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7738630. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539458 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 33.777 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_5047_length_23002_cov_19.472715 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_5047_length_23002_cov_19.472715 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738161_provirus.435 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11141426 SAMEA13539459 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr130_1 virus assembled from ERR7738630. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539459 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 270.474 MAG coverage software Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_D_12_1182__NODE_710_length_97650_cov_147.080606 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5490196078431373 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585605 sample name Hadza_MoBio_hadza-I-L_D_12_1182__NODE_710_length_97650_cov_147.080606 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268072 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella stercorea vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.710 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr130_1 virus enrichment approach none ERS11141427 SAMEA13539460 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738631. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539460 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 36.4246 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 72 Number of CRISPR spacer hits supporting host taxonomy 282 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1086_length_59406_cov_23.582531_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1086_length_59406_cov_23.582531_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141428 SAMEA13539461 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738631. BACPHLIP temperate score 0.23799472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539461 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:27Z INSDC last update 2022-12-27T00:30:27Z INSDC status public MAG coverage depth 16.3288 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_220_length_144485_cov_10.227958_1 Viral contig found in MAG ERR7738631_bin.202 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_220_length_144485_cov_10.227958_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124681 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__CAG-115 sp000432175 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_provirus.220 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141429 SAMEA13539462 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738631. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539462 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 54.5177 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 258 Number of CRISPR spacer hits supporting host taxonomy 227 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_384_length_112502_cov_35.963353_1 Viral contig found in MAG ERR7738631_bin.30 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9318181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_384_length_112502_cov_35.963353_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0367225 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141430 SAMEA13539463 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738631. BACPHLIP temperate score 0.00247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539463 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 91.488 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_685_length_81055_cov_61.143261_1 Viral contig found in MAG ERR7738631_bin.30 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_685_length_81055_cov_61.143261_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745403_provirus.913 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141431 SAMEA13539464 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539464 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 94.3777 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1101_length_58730_cov_58.095051 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9629629629629628 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1101_length_58730_cov_58.095051 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME261446 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp003538135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.1101 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141432 SAMEA13539465 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539465 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 16.5869 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1431_length_48487_cov_10.124726 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9736842105263158 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1431_length_48487_cov_10.124726 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747083_virus.752 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141433 SAMEA13539466 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539466 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 207.981 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 460 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1646_length_43573_cov_127.678798 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.4827586206896552 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1646_length_43573_cov_127.678798 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738242_virus.549 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141434 SAMEA13539467 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539467 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 55.8827 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1824_length_40335_cov_35.537831 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_1824_length_40335_cov_35.537831 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738241_virus.1176 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141435 SAMEA13539468 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539468 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 23.075 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_2013_length_37589_cov_14.315632 Viral contig found in MAG ERR7738631_bin.241 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_2013_length_37589_cov_14.315632 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738584_bin.110 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.2013 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141436 SAMEA13539469 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539469 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 23.4962 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_270_length_133210_cov_14.493206 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6458333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_270_length_133210_cov_14.493206 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.247 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141437 SAMEA13539470 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539470 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 8.36396 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 115 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_4393_length_20240_cov_5.028666 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_4393_length_20240_cov_5.028666 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253237 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465;s__CAG-465 sp000433755 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_provirus.53 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141438 SAMEA13539471 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7738631. BACPHLIP temperate score 0.12878892628021937 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539471 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 61.8641 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_501_length_98778_cov_38.059999 Viral contig found in MAG ERR7738631_bin.47 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_501_length_98778_cov_38.059999 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746012_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11141439 SAMEA13539472 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539472 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 21.1371 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_652_length_83643_cov_13.150600 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4583333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_652_length_83643_cov_13.150600 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.652 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141440 SAMEA13539473 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738631. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539473 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 61.1103 MAG coverage software Reads (ERR7738631) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561193) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-A-D_B_6_1603__NODE_872_length_69528_cov_38.205008 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.6590909090909091 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585852 sample name Hadza_MoBio_hadza-A-D_B_6_1603__NODE_872_length_69528_cov_38.205008 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.763 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141441 SAMEA13539474 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738633. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539474 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 10.7519 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 333 Number of CRISPR spacer hits supporting host taxonomy 161 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1339_length_56718_cov_5.835049_1 Viral contig found in MAG ERR7738633_bin.87 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.96875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1339_length_56718_cov_5.835049_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0239997 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141442 SAMEA13539475 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus provirus assembled from ERR7738633. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539475 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:28Z INSDC last update 2022-12-27T00:30:28Z INSDC status public MAG coverage depth 33.61 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 390 Number of CRISPR spacer hits supporting host taxonomy 152 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1489_length_52254_cov_24.068862_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.26666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1489_length_52254_cov_24.068862_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738633_provirus.1489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141444 SAMEA13539477 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738633. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539477 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 15.5112 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 94 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_579_length_102393_cov_8.649947_1 Viral contig found in MAG ERR7738633_bin.181 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_579_length_102393_cov_8.649947_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0251556 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141445 SAMEA13539478 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 provirus assembled from ERR7738633. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539478 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 194.998 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 319 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_80_length_287853_cov_109.143907_1 Viral contig found in MAG ERR7738633_bin.56 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2916666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_80_length_287853_cov_109.143907_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME261564 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__Alistipes onderdonkii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738633_provirus.80 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11141446 SAMEA13539479 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738633. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539479 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 31.1358 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1319_length_57251_cov_17.680152 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9130434782608696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1319_length_57251_cov_17.680152 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0345861 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141447 SAMEA13539480 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738633. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539480 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 594.092 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3023 Number of CRISPR spacer hits supporting host taxonomy 102 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1663_length_47739_cov_335.225106 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_1663_length_47739_cov_335.225106 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001734 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides uniformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0335683 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141448 SAMEA13539481 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738633. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539481 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 893.385 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 502 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_2133_length_38552_cov_516.065367 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_2133_length_38552_cov_516.065367 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0318076 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141450 SAMEA13539483 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7738633. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539483 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 331.437 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 388 Number of CRISPR spacer hits supporting host taxonomy 1008 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_3008_length_27982_cov_183.799892 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6071428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_3008_length_27982_cov_183.799892 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11141451 SAMEA13539484 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7738633. BACPHLIP temperate score 0.09677917672702029 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539484 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 8.2059 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_4132_length_20203_cov_4.401669 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_4132_length_20203_cov_4.401669 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0266477 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11141452 SAMEA13539485 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738633. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539485 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 1762.35 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_621_length_97849_cov_976.126192 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_621_length_97849_cov_976.126192 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147876 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides merdae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0378020 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141453 SAMEA13539486 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738643. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539486 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 54.1959 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 506 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1333_length_57740_cov_32.755805_1 Viral contig found in MAG ERR7738643_bin.256 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 85.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9666666666666668 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1333_length_57740_cov_32.755805_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_provirus.360 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141454 SAMEA13539487 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738643. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539487 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 32.896 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 88 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1796_length_47414_cov_19.238883_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1796_length_47414_cov_19.238883_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024263 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides sp900549585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_provirus.1796 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141455 SAMEA13539488 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738643. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539488 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 14.6735 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_296_length_135861_cov_8.302974_1 Viral contig found in MAG ERR7738643_bin.361 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_296_length_135861_cov_8.302974_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738591_bin.140 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter;s__Oxalobacter sp900760095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_provirus.296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141456 SAMEA13539489 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn provirus assembled from ERR7738643. BACPHLIP temperate score 0.0699339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539489 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 70.9742 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 294 Number of CRISPR spacer hits supporting host taxonomy 497 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_510_length_102579_cov_41.683684_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_510_length_102579_cov_41.683684_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11141457 SAMEA13539490 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539490 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 15.3154 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1058_length_67268_cov_8.631201 Viral contig found in MAG ERR7738643_bin.334 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5945945945945946 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1058_length_67268_cov_8.631201 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1058 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141459 SAMEA13539492 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539492 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 56.1114 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1553_length_52281_cov_31.882270 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1553_length_52281_cov_31.882270 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738643_bin.213 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__UBA644;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.816 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141460 SAMEA13539493 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539493 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 58.5667 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 123 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1852_length_46401_cov_33.103985 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1852_length_46401_cov_33.103985 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1852 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141461 SAMEA13539494 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.6875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539494 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 11.5473 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1985_length_44276_cov_6.491663 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1985_length_44276_cov_6.491663 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1985 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141462 SAMEA13539495 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539495 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 28.5162 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2110_length_42443_cov_16.216117 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2110_length_42443_cov_16.216117 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__MARSEILLE-P3954;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.2110 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141463 SAMEA13539496 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539496 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 14.3263 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2223_length_40864_cov_7.970334 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2223_length_40864_cov_7.970334 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_virus.1013 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141465 SAMEA13539498 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738643. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539498 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 28.783 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_248_length_147750_cov_16.290182 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.8035714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_248_length_147750_cov_16.290182 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp003514385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.248 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141466 SAMEA13539499 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539499 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 17.1735 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2705_length_35901_cov_9.822047 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2705_length_35901_cov_9.822047 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.2061 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141467 SAMEA13539500 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539500 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 79.9237 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_306_length_134273_cov_47.309026 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.45714285714285713 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_306_length_134273_cov_47.309026 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.306 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141468 SAMEA13539501 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539501 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 10.8853 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_3682_length_28592_cov_6.198036 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_3682_length_28592_cov_6.198036 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745594_bin.118 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;s__UBA636 sp900546285 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.3682 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141469 SAMEA13539502 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539502 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 9.19539 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_4292_length_25259_cov_5.118696 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_4292_length_25259_cov_5.118696 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.2618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141470 SAMEA13539503 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus virus assembled from ERR7738643. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539503 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 8.51528 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_4947_length_22530_cov_4.864829 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_4947_length_22530_cov_4.864829 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.4947 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11141471 SAMEA13539504 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7738643. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539504 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 216.01 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 123 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_578_length_93687_cov_127.979853 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9302325581395348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_578_length_93687_cov_127.979853 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.578 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11141473 SAMEA13539506 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738645. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539506 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 36.1405 MAG coverage software Reads (ERR7738645) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_11_length_385521_cov_22.112771_1 Viral contig found in MAG ERR7738645_bin.102 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9655172413793104 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787395 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_11_length_385521_cov_22.112771_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME233192 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus ruminis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738645_provirus.11 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141474 SAMEA13539507 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738645. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539507 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 10.6189 MAG coverage software Reads (ERR7738645) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_423_length_64776_cov_6.185536_1 Viral contig found in MAG ERR7738645_bin.41 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787395 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_423_length_64776_cov_6.185536_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147876 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides merdae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0267854 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141475 SAMEA13539508 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738645. BACPHLIP temperate score 0.06390472738781326 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13539508 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-28T19:46:17Z INSDC status public MAG coverage depth 7.43836 MAG coverage software Reads (ERR7738645) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 363 Number of CRISPR spacer hits supporting host taxonomy 114 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_1230_length_29135_cov_4.250981 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787395 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_1230_length_29135_cov_4.250981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0236306 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141476 SAMEA13539509 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738645. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539509 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 40.3828 MAG coverage software Reads (ERR7738645) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 322 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_309_length_79927_cov_24.238610 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787395 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_309_length_79927_cov_24.238610 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738645_virus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141477 SAMEA13539510 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738645. BACPHLIP temperate score 0.4875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539510 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 15.1203 MAG coverage software Reads (ERR7738645) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 515 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_575_length_53357_cov_8.901802 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7878787878787878 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787395 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_575_length_53357_cov_8.901802 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0321081 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141479 SAMEA13539512 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738651. BACPHLIP temperate score 0.08997797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539512 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 26.3128 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_105_length_189621_cov_16.281133_1 Viral contig found in MAG ERR7738651_bin.256 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 48.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_105_length_189621_cov_16.281133_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_provirus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141480 SAMEA13539513 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738651. BACPHLIP temperate score 0.15001018949221068 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539513 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 21.1959 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1930_length_44500_cov_12.667154_1 Viral contig found in MAG ERR7738651_bin.131 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1930_length_44500_cov_12.667154_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.1673 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141481 SAMEA13539514 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738651. BACPHLIP temperate score 0.24217479228380095 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539514 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 38.9233 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 689 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_3388_length_29636_cov_26.713996_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_3388_length_29636_cov_26.713996_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_provirus.3388 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141482 SAMEA13539515 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738651. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539515 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 10.2057 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_4360_length_24483_cov_6.034049_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_4360_length_24483_cov_6.034049_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145587 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A;s__Slackia_A isoflavoniconvertens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_provirus.248 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141483 SAMEA13539516 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738651. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539516 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 46.2684 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_911_length_69980_cov_27.794530_1 Viral contig found in MAG ERR7738651_bin.264 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_911_length_69980_cov_27.794530_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746344_virus.1947 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141484 SAMEA13539517 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738651. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539517 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 213.558 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1157_length_61557_cov_128.232824 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1157_length_61557_cov_128.232824 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME157359 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA3388;s__UBA3388 sp900545215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_provirus.172 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141485 SAMEA13539518 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738651. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539518 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 52.3814 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 107 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1469_length_53146_cov_32.849291 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42105263157894735 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1469_length_53146_cov_32.849291 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1469 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141486 SAMEA13539519 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738651. BACPHLIP temperate score 0.5875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539519 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 41.509 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 322 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1737_length_47895_cov_24.973420 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_1737_length_47895_cov_24.973420 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1737 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141488 SAMEA13539521 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539521 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 45.4631 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2313_length_39168_cov_33.746898 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2313_length_39168_cov_33.746898 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746692_virus.650 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141489 SAMEA13539522 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539522 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 74.4174 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2665_length_35594_cov_45.014219 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2665_length_35594_cov_45.014219 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME026639 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900548625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.2665 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141490 SAMEA13539523 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539523 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 13.202 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2917_length_33367_cov_7.879003 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9032258064516128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2917_length_33367_cov_7.879003 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.2917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141491 SAMEA13539524 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738651. BACPHLIP temperate score 0.5255538234328847 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539524 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 52.2469 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_331_length_116978_cov_32.639781 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.8985507246376812 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_331_length_116978_cov_32.639781 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_provirus.176 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141492 SAMEA13539525 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 0.04730176211453744 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539525 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 9.03181 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_4081_length_25710_cov_5.463348 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_4081_length_25710_cov_5.463348 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.4081 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141494 SAMEA13539527 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 0.02425715029530222 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539527 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 8.90661 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_5165_length_21363_cov_5.356525 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_5165_length_21363_cov_5.356525 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738179_virus.1723 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141495 SAMEA13539528 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 0.04805480131144586 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539528 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 473.717 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_6999_length_16637_cov_290.403744 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_6999_length_16637_cov_290.403744 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_provirus.586 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141496 SAMEA13539529 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738653. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539529 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 35.9288 MAG coverage software Reads (ERR7738653) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567268) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1134 Number of CRISPR spacer hits supporting host taxonomy 357 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_102_length_101035_cov_22.336774_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 11 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.6792452830188679 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787385 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_102_length_101035_cov_22.336774_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738653_provirus.102 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141497 SAMEA13539530 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738653. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539530 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 7.86532 MAG coverage software Reads (ERR7738653) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567268) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_317_length_57828_cov_4.737979_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8620689655172413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787385 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_317_length_57828_cov_4.737979_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738564_virus.149 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141498 SAMEA13539531 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738653. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539531 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 8.04486 MAG coverage software Reads (ERR7738653) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567268) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 685 Number of CRISPR spacer hits supporting host taxonomy 138 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_781_length_30757_cov_4.789276_1 Viral contig found in MAG ERR7738653_bin.85 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787385 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_781_length_30757_cov_4.789276_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738653_provirus.781 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141499 SAMEA13539532 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738653. BACPHLIP temperate score 0.675 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539532 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 43.092 MAG coverage software Reads (ERR7738653) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567268) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 540 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_324_length_56949_cov_26.568276 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787385 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_5_RAU0022YZ__NODE_324_length_56949_cov_26.568276 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738653_virus.324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141501 SAMEA13539534 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738657. BACPHLIP temperate score 0.18308091782530816 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539534 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 51.1762 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 53 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_161_length_178384_cov_30.953900_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_161_length_178384_cov_30.953900_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME273772 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__RUG841;s__RUG841 sp900313795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_provirus.161 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141502 SAMEA13539535 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738657. BACPHLIP temperate score 0.05883159685814017 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539535 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 14.7749 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_224_length_158995_cov_8.481437_1 Viral contig found in MAG ERR7738657_bin.318 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_224_length_158995_cov_8.481437_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_provirus.224 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141503 SAMEA13539536 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738657. BACPHLIP temperate score 0.00247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539536 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 9.3553 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_3025_length_37575_cov_5.435970_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 48.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_3025_length_37575_cov_5.435970_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745414_bin.186 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900768625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_provirus.348 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141504 SAMEA13539537 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738657. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539537 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 56.2814 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_494_length_112167_cov_32.878357_1 Viral contig found in MAG ERR7738657_bin.48 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_494_length_112167_cov_32.878357_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738230_bin.158 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745419_virus.1042 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141505 SAMEA13539538 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738657. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539538 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 49.2984 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_811_length_87042_cov_28.584120_1 Viral contig found in MAG ERR7738657_bin.279 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_811_length_87042_cov_28.584120_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.29 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900554205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_provirus.327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141507 SAMEA13539540 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539540 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 14.3327 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1378_length_63830_cov_8.117955 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1378_length_63830_cov_8.117955 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738630_bin.313 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFFH01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.1378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141508 SAMEA13539541 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539541 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 63.5349 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1636_length_57143_cov_35.952984 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9767441860465116 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1636_length_57143_cov_35.952984 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.1636 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141509 SAMEA13539542 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.827477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539542 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 35.3458 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 616 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1862_length_53217_cov_21.131916 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1862_length_53217_cov_21.131916 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141510 SAMEA13539543 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539543 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 9.7334 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_2548_length_42693_cov_5.352661 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_2548_length_42693_cov_5.352661 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745858_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__UMGS1670;s__UMGS1670 sp900553995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.2548 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141511 SAMEA13539544 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738657. BACPHLIP temperate score 0.07725770925110134 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539544 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 7.05333 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_2843_length_39512_cov_4.043667 Viral contig found in MAG ERR7738657_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 67.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_2843_length_39512_cov_4.043667 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-977;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.526 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141512 SAMEA13539545 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539545 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 50.3913 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_3095_length_36910_cov_29.292699 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_3095_length_36910_cov_29.292699 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME110466 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900546925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.3095 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141513 SAMEA13539546 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539546 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 9.77967 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_3508_length_33632_cov_5.500611 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_3508_length_33632_cov_5.500611 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.3508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141514 SAMEA13539547 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738657. BACPHLIP temperate score 0.864977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539547 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 28.3971 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_4120_length_29702_cov_16.757401 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_4120_length_29702_cov_16.757401 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.832 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141515 SAMEA13539548 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539548 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 7.86894 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_4808_length_26345_cov_4.310644 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_4808_length_26345_cov_4.310644 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_virus.1413 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11141517 SAMEA13539550 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738657. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539550 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 12.3461 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 478 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_6222_length_21251_cov_7.474922 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_6222_length_21251_cov_7.474922 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000434975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_provirus.717 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141518 SAMEA13539551 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738657. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539551 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 87.3589 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_755_length_90440_cov_50.271062 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6388888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_755_length_90440_cov_50.271062 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.755 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141519 SAMEA13539552 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738657. BACPHLIP temperate score 0.11722655367650484 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539552 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 24.8333 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_9088_length_15541_cov_14.475168 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_9088_length_15541_cov_14.475168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.9088 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141520 SAMEA13539553 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738659. BACPHLIP temperate score 0.1998898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539553 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 57.0418 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 152 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_126_length_183778_cov_32.280929_1 Viral contig found in MAG ERR7738659_bin.278 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_126_length_183778_cov_32.280929_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141521 SAMEA13539554 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738659. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539554 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 76.5398 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_1817_length_44429_cov_43.426565_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_1817_length_44429_cov_43.426565_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.671 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141523 SAMEA13539556 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738659. BACPHLIP temperate score 0.06862117793506581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539556 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 28.9425 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_522_length_91361_cov_17.956849_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_522_length_91361_cov_17.956849_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.1178 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141524 SAMEA13539557 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7738659. BACPHLIP temperate score 0.06321814991225902 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539557 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 24.621 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_894_length_69593_cov_14.694962_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_894_length_69593_cov_14.694962_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_provirus.810 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141525 SAMEA13539558 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738659. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539558 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 52.027 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_1155_length_58649_cov_45.401079 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_1155_length_58649_cov_45.401079 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745384_bin.138 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900553155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.1155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141526 SAMEA13539559 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738659. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539559 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 26.8593 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 287 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_1769_length_45026_cov_15.244477 Viral contig found in MAG ERR7738659_bin.160 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_1769_length_45026_cov_15.244477 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME277835 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__CAG-269 sp000437215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.1769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141527 SAMEA13539560 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738659. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539560 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 67.3411 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_2129_length_39951_cov_37.847821 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_2129_length_39951_cov_37.847821 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746051_bin.216 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger variabilis_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738221_virus.807 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141528 SAMEA13539561 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738659. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539561 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 240.086 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 209 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_2602_length_34482_cov_134.511554 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_2602_length_34482_cov_134.511554 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738575_bin.23 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-279;s__CAG-279 sp000437795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_virus.618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141529 SAMEA13539562 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738659. BACPHLIP temperate score 0.0322136563876652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539562 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 20.1072 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_3090_length_30241_cov_11.263824 Viral contig found in MAG ERR7738659_bin.147 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_3090_length_30241_cov_11.263824 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.3090 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141531 SAMEA13539564 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738659. BACPHLIP temperate score 0.0574339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539564 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 7.61145 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_5572_length_18706_cov_4.172044 Viral contig found in MAG ERR7738659_bin.146 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_5572_length_18706_cov_4.172044 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.5572 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141532 SAMEA13539565 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738659. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539565 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 6.5811 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_9032_length_12246_cov_3.533733 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_9032_length_12246_cov_3.533733 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.2423 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141533 SAMEA13539566 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738660. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539566 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 13.1839 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1402_length_52897_cov_7.473911_1 Viral contig found in MAG ERR7738660_bin.209 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1402_length_52897_cov_7.473911_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738660_provirus.1402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141534 SAMEA13539567 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738660. BACPHLIP temperate score 0.0998898678414097 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539567 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 21.1701 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1915_length_43654_cov_12.358974_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1915_length_43654_cov_12.358974_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_virus.1263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141535 SAMEA13539568 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738660. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539568 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 13.3819 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_2895_length_33994_cov_7.839225_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_2895_length_33994_cov_7.839225_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_provirus.583 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141537 SAMEA13539570 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738660. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539570 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 20.1691 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 84 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_837_length_70477_cov_11.620810_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_837_length_70477_cov_11.620810_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.1803 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141538 SAMEA13539571 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539571 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 9.71874 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1164_length_58633_cov_5.503364 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; HMM-based (lower-bound) completeness score 52.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1164_length_58633_cov_5.503364 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_virus.190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141539 SAMEA13539572 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738660. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539572 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 13.8487 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 390 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1600_length_48767_cov_8.439433 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1600_length_48767_cov_8.439433 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_virus.236 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141540 SAMEA13539573 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539573 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 12.2019 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1988_length_42622_cov_7.104689 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_1988_length_42622_cov_7.104689 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738660_virus.1988 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141541 SAMEA13539574 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539574 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 36.806 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_2406_length_38044_cov_22.647036 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_2406_length_38044_cov_22.647036 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738660_virus.2406 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141542 SAMEA13539575 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.01495011113590989 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539575 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 31.8605 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_2658_length_35853_cov_19.593806 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_2658_length_35853_cov_19.593806 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.1008 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141543 SAMEA13539576 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539576 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 12.524 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 1256 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_3387_length_30790_cov_7.254355 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_3387_length_30790_cov_7.254355 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_provirus.188 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141544 SAMEA13539577 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539577 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 30.9323 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_3956_length_27863_cov_18.091845 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_3956_length_27863_cov_18.091845 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_provirus.155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141363 SAMEA13539395 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7738626. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539395 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:21Z INSDC last update 2022-12-27T00:30:21Z INSDC status public MAG coverage depth 264.427 MAG coverage software Reads (ERR7738626) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560783) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-E-H_E_17_1727__NODE_783_length_95353_cov_149.218250 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.967741935483871 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585970 sample name Hadza_MoBio_hadza-E-H_E_17_1727__NODE_783_length_95353_cov_149.218250 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.669 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11141443 SAMEA13539476 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738633. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13539476 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-28T19:46:15Z INSDC status public MAG coverage depth 66.1396 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_2187_length_37837_cov_37.214619_1 Viral contig found in MAG ERR7738633_bin.158 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_2187_length_37837_cov_37.214619_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143232 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides cellulosilyticus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738549_virus.1198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141449 SAMEA13539482 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738633. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539482 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 301.851 MAG coverage software Reads (ERR7738633) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558881) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 143 Number of CRISPR spacer hits supporting host taxonomy 143 Submitter Id Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_2444_length_34072_cov_171.826857 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383820 sample name Pilot_MoBio_Fiber-Hadza-Nepal_M_3_7038__NODE_2444_length_34072_cov_171.826857 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380186 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141458 SAMEA13539491 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539491 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 48.5135 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1402_length_55740_cov_27.818964 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_1402_length_55740_cov_27.818964 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1402 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141464 SAMEA13539497 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738643. BACPHLIP temperate score 0.04988986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539497 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 19.752 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2383_length_38988_cov_11.314436 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; HMM-based (lower-bound) completeness score 75.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_2383_length_38988_cov_11.314436 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME041878 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__CAG-1024;s__CAG-1024 sp000432015 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_virus.898 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141472 SAMEA13539505 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738643. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539505 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 8.45121 MAG coverage software Reads (ERR7738643) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560103) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_21_2150__NODE_7467_length_16167_cov_4.642014 Viral contig found in MAG ERR7738643_bin.310 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586136 sample name Hadza_MoBio_hadza-E-H_P_21_2150__NODE_7467_length_16167_cov_4.642014 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.7467 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141478 SAMEA13539511 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738645. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539511 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T00:30:31Z INSDC last update 2022-12-27T00:30:31Z INSDC status public MAG coverage depth 40.9205 MAG coverage software Reads (ERR7738645) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567408) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 249 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_834_length_39486_cov_24.848588 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787395 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_7_THA0058AZ__NODE_834_length_39486_cov_24.848588 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0288732 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141487 SAMEA13539520 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539520 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 403.312 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 608 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2027_length_42937_cov_247.536771 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_2027_length_42937_cov_247.536771 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.2027 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141493 SAMEA13539526 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738651. BACPHLIP temperate score 0.1931310196624605 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539526 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 9.42055 MAG coverage software Reads (ERR7738651) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560070) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_9_2144__NODE_4565_length_23636_cov_5.582622 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586130 sample name Hadza_MoBio_hadza-E-H_P_9_2144__NODE_4565_length_23636_cov_5.582622 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.4565 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141500 SAMEA13539533 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738657. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539533 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 26.2593 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 76 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1060_length_75272_cov_15.740049_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_1060_length_75272_cov_15.740049_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0357521 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141506 SAMEA13539539 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539539 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 10.6306 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_10911_length_13259_cov_5.962828 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_10911_length_13259_cov_5.962828 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.10911 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141516 SAMEA13539549 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738657. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539549 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 7.42707 MAG coverage software Reads (ERR7738657) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Hadza_MoBio_hadza-E-H_G_5_1733__NODE_5624_length_23165_cov_4.119499 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585976 sample name Hadza_MoBio_hadza-E-H_G_5_1733__NODE_5624_length_23165_cov_4.119499 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0370468 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141522 SAMEA13539555 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738659. BACPHLIP temperate score 0.6799559471365638 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539555 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 157.343 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_326_length_116635_cov_91.101735_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_326_length_116635_cov_91.101735_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.72 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141530 SAMEA13539563 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738659. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539563 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 11.2576 MAG coverage software Reads (ERR7738659) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560611) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_H_22_1650__NODE_4373_length_22864_cov_6.396717 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_MoBio_hadza-A-D_H_22_1650__NODE_4373_length_22864_cov_6.396717 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME171351 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella;s__Veillonella parvula_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.4373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141536 SAMEA13539569 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738660. BACPHLIP temperate score 0.08210352422907494 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539569 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 8.47235 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_4003_length_27621_cov_4.697611_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_4003_length_27621_cov_4.697611_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_provirus.1432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141545 SAMEA13539578 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.0932209057437508 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539578 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 29.6942 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_4884_length_24198_cov_20.023672 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_4884_length_24198_cov_20.023672 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.224 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__Ruminococcus sp900540005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738240_virus.1786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141546 SAMEA13539579 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.21619739868756788 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539579 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 19.6002 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 98 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_6524_length_19907_cov_13.878719 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_6524_length_19907_cov_13.878719 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_provirus.917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141547 SAMEA13539580 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738660. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539580 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 51.7548 MAG coverage software Reads (ERR7738660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567818) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_8364_length_16734_cov_30.644294 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; HMM-based (lower-bound) completeness score 56.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585780 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_8_1525__NODE_8364_length_16734_cov_30.644294 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.4855 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141548 SAMEA13539581 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738661. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539581 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 20.5184 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1525_length_61350_cov_12.835115_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1525_length_61350_cov_12.835115_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738579_provirus.1307 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141549 SAMEA13539582 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738661. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539582 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:10Z INSDC last update 2022-12-27T19:09:10Z INSDC status public MAG coverage depth 22.2568 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2343_length_46388_cov_13.547386_1 Viral contig found in MAG ERR7738661_bin.10 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2343_length_46388_cov_13.547386_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746398_bin.161 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;s__Oribacterium sp900772695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_provirus.2343 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141550 SAMEA13539583 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738661. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539583 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 13.1332 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 266 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_3120_length_37039_cov_7.864509_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_3120_length_37039_cov_7.864509_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140786 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D bicirculans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_provirus.3120 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141551 SAMEA13539584 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738661. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539584 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 445.108 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 101 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_603_length_110119_cov_258.126215_1 Viral contig found in MAG ERR7738661_bin.218 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_603_length_110119_cov_258.126215_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.1446 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141552 SAMEA13539585 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738661. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539585 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 25.0509 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1145 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1202_length_72388_cov_15.287439 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1202_length_72388_cov_15.287439 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.1202 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141553 SAMEA13539586 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.6375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539586 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 73.1278 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1429_length_64160_cov_42.792254 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9736842105263158 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1429_length_64160_cov_42.792254 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.1429 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141554 SAMEA13539587 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539587 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 710.091 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1640_length_58735_cov_414.649715 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9722222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1640_length_58735_cov_414.649715 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.1640 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141555 SAMEA13539588 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738661. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539588 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 97.1844 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1864_length_53952_cov_58.621698 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_1864_length_53952_cov_58.621698 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738207_virus.383 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141556 SAMEA13539589 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.17129856875493005 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539589 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 112.639 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2094_length_50292_cov_65.716698 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2094_length_50292_cov_65.716698 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.2094 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141557 SAMEA13539590 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7738661. BACPHLIP temperate score 0.1820121253599783 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539590 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 41.9305 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_240_length_169652_cov_24.171269 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_240_length_169652_cov_24.171269 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.108 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141558 SAMEA13539591 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539591 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 17.5518 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2517_length_43834_cov_10.288845 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2517_length_43834_cov_10.288845 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.2245 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141559 SAMEA13539592 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539592 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 36.1884 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2654_length_41917_cov_21.127749 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2654_length_41917_cov_21.127749 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.2654 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141560 SAMEA13539593 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539593 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 25.9439 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2830_length_40096_cov_15.109798 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2830_length_40096_cov_15.109798 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.2830 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141561 SAMEA13539594 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539594 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 32.7882 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 64 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2998_length_38172_cov_19.994619 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_2998_length_38172_cov_19.994619 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.2998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141562 SAMEA13539595 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.55 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539595 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 8.05689 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_3203_length_36166_cov_4.519244 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_3203_length_36166_cov_4.519244 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738553_bin.131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.3203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141563 SAMEA13539596 336724 Myoviridae environmental samples This sample represents an uncultured Pbunavirus virus assembled from ERR7738661. BACPHLIP temperate score 0.11701541850220272 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539596 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 201.144 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_3723_length_32109_cov_117.807224 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_3723_length_32109_cov_117.807224 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.3723 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Pbunavirus virus enrichment approach none ERS11141564 SAMEA13539597 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539597 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 1434.39 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_430_length_131134_cov_825.191298 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_430_length_131134_cov_825.191298 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.292 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141565 SAMEA13539598 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539598 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 36.8499 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 77 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_49_length_318951_cov_22.299877 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; HMM-based (lower-bound) completeness score 98.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.4189189189189189 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_49_length_318951_cov_22.299877 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746349_bin.313 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95;s__CAG-95 sp000436115 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.49 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141566 SAMEA13539599 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 0.1389047273878133 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539599 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 14.2754 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_5768_length_21960_cov_8.851254 Viral contig found in MAG ERR7738661_bin.227 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_5768_length_21960_cov_8.851254 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.5768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141567 SAMEA13539600 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738661. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539600 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 55.5313 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 150 Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_696_length_99931_cov_32.971508 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_696_length_99931_cov_32.971508 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738203_virus.209 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141568 SAMEA13539601 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738661. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539601 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 24.124 MAG coverage software Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_7_2143__NODE_832_length_89973_cov_13.829025 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586129 sample name Hadza_MoBio_hadza-E-H_P_7_2143__NODE_832_length_89973_cov_13.829025 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141569 SAMEA13539602 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738662. BACPHLIP temperate score 0.05938930888561059 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539602 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 41.4339 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 312 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_1016_length_64100_cov_24.837449_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5897435897435898 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_1016_length_64100_cov_24.837449_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0347707 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141570 SAMEA13539603 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738662. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539603 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 290.812 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 298 Number of CRISPR spacer hits supporting host taxonomy 186 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_220_length_169769_cov_180.897343_1 Viral contig found in MAG ERR7738662_bin.59 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_220_length_169769_cov_180.897343_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0341270 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141571 SAMEA13539604 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus provirus assembled from ERR7738662. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539604 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 877.444 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 362 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_469_length_114623_cov_520.939483_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_469_length_114623_cov_520.939483_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0354100 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11141572 SAMEA13539605 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738662. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539605 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 85.2215 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 86 Number of CRISPR spacer hits supporting host taxonomy 858 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_797_length_78610_cov_51.147034_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6410256410256411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_797_length_78610_cov_51.147034_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0313669 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141573 SAMEA13539606 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738662. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539606 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 50.7704 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 202 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_1498_length_45207_cov_29.822358 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_1498_length_45207_cov_29.822358 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738662_virus.1498 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141574 SAMEA13539607 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu virus assembled from ERR7738662. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539607 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 13.2693 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 275 Number of CRISPR spacer hits supporting host taxonomy 623 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_1855_length_36803_cov_7.826281 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_1855_length_36803_cov_7.826281 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.698 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11141575 SAMEA13539608 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738662. BACPHLIP temperate score 0.03986784140969163 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539608 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 6.59727 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_3333_length_19828_cov_3.653638 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_3333_length_19828_cov_3.653638 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME158963 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS856;s__UMGS856 sp900546265 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738662_virus.3333 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141576 SAMEA13539609 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738662. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539609 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 35.411 MAG coverage software Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 192 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_972_length_66412_cov_20.951413 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787382 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ__NODE_972_length_66412_cov_20.951413 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738662_virus.972 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141577 SAMEA13539610 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738664. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539610 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 25.058 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_196_length_149285_cov_17.707777_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_196_length_149285_cov_17.707777_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_provirus.196 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141578 SAMEA13539611 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738664. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539611 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 20.3063 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_351_length_115285_cov_11.727042_1 Viral contig found in MAG ERR7738664_bin.215 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_351_length_115285_cov_11.727042_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_provirus.351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141579 SAMEA13539612 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738664. BACPHLIP temperate score 0.19367550097940467 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539612 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 10.8411 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 80 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_512_length_98705_cov_6.261711_1 Viral contig found in MAG ERR7738664_bin.299 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_512_length_98705_cov_6.261711_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738193_provirus.11 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141580 SAMEA13539613 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7738664. BACPHLIP temperate score 0.1621696035242291 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539613 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 144.068 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_851_length_75820_cov_83.597243_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_851_length_75820_cov_83.597243_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_provirus.1304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141581 SAMEA13539614 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738664. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539614 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 367.802 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_1147_length_63032_cov_213.025034 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9210526315789472 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_1147_length_63032_cov_213.025034 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159485 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_virus.594 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141582 SAMEA13539615 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738664. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539615 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 12.4209 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 133 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_1724_length_48434_cov_7.274583 Viral contig found in MAG ERR7738664_bin.288 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_1724_length_48434_cov_7.274583 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.1527 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141583 SAMEA13539616 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738664. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539616 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 28.7881 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_2071_length_42316_cov_16.946092 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_2071_length_42316_cov_16.946092 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_virus.2071 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141584 SAMEA13539617 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738664. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539617 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 37.1933 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_2375_length_38317_cov_21.651464 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_2375_length_38317_cov_21.651464 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_virus.2375 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141585 SAMEA13539618 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738664. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539618 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 35.8733 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 133 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_2798_length_33989_cov_20.744309 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_2798_length_33989_cov_20.744309 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745545_virus.1252 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141586 SAMEA13539619 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738664. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539619 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 34.7491 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 557 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_428_length_106650_cov_20.271542 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.25 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_428_length_106650_cov_20.271542 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_virus.428 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141587 SAMEA13539620 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738664. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539620 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 137.787 MAG coverage software Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 351 Submitter Id Hadza_MoBio_hadza-I-L_K_16_2625__NODE_647_length_87174_cov_80.318289 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586334 sample name Hadza_MoBio_hadza-I-L_K_16_2625__NODE_647_length_87174_cov_80.318289 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745545_virus.231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141588 SAMEA13539621 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738665. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539621 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 97.8469 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 152 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_1234_length_80781_cov_71.516368_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7045454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_1234_length_80781_cov_71.516368_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0318097 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141589 SAMEA13539622 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738665. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539622 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:09Z INSDC last update 2022-12-27T19:09:09Z INSDC status public MAG coverage depth 23.3197 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_1573_length_68925_cov_14.380026_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9069767441860463 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_1573_length_68925_cov_14.380026_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738665_provirus.1573 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141590 SAMEA13539623 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7738665. BACPHLIP temperate score 0.18997797356828192 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539623 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 42.9225 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 418 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_200_length_202183_cov_25.621802_1 Viral contig found in MAG ERR7738665_bin.242 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_200_length_202183_cov_25.621802_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0348753 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141591 SAMEA13539624 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738665. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539624 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 9.39021 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 122 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_2476_length_49159_cov_5.484577_1 Viral contig found in MAG ERR7738665_bin.365 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_2476_length_49159_cov_5.484577_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME121515 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20;s__51-20 sp001917175 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0244827 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141592 SAMEA13539625 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738665. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539625 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 446.319 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 125 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_384_length_152183_cov_265.505417_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.55 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_384_length_152183_cov_265.505417_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME246707 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__Phil1;s__Phil1 sp001940855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_provirus.70 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141593 SAMEA13539626 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738665. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539626 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 18.0242 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_547_length_128425_cov_10.800355_1 Viral contig found in MAG ERR7738665_bin.270 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_547_length_128425_cov_10.800355_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147876 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides merdae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738665_provirus.547 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141594 SAMEA13539627 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738665. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539627 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 35.2967 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 533 Number of CRISPR spacer hits supporting host taxonomy 148 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_878_length_98088_cov_20.774566_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_878_length_98088_cov_20.774566_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096193 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;s__Mediterraneibacter torques vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738665_provirus.878 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141595 SAMEA13539628 336724 Myoviridae environmental samples This sample represents an uncultured Phage DP SC_6_H4_2017 virus assembled from ERR7738665. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539628 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 290.828 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_1162_length_83070_cov_170.444495 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_1162_length_83070_cov_170.444495 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME258505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0356247 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Phage DP SC_6_H4_2017 virus enrichment approach none ERS11141596 SAMEA13539629 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738665. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539629 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 254.111 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 455 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_2054_length_56731_cov_150.924295 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_2054_length_56731_cov_150.924295 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738546_virus.1270 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141597 SAMEA13539630 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738665. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539630 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 25.9633 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_2421_length_50040_cov_15.464784 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_2421_length_50040_cov_15.464784 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.161 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900545925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738546_virus.621 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141598 SAMEA13539631 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738665. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539631 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 46.3896 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_2739_length_45235_cov_27.765712 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6129032258064516 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_2739_length_45235_cov_27.765712 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257069 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella;s__Fournierella sp900543285 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0311266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141599 SAMEA13539632 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738665. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539632 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 12.2135 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_3308_length_38776_cov_7.237551 Viral contig found in MAG ERR7738665_bin.327 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_3308_length_38776_cov_7.237551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME114842 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS731;s__UMGS731 sp900544985 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738665_virus.3308 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141600 SAMEA13539633 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738665. BACPHLIP temperate score 0.19672273990657685 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539633 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 349.472 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_3559_length_36459_cov_207.029080 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_3559_length_36459_cov_207.029080 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253835 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A;s__Alistipes_A ihumii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0269636 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141601 SAMEA13539634 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738665. BACPHLIP temperate score 0.04666904456842997 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539634 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 8.0187 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_4389_length_30309_cov_4.627779 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_4389_length_30309_cov_4.627779 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738665_virus.4389 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141602 SAMEA13539635 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738665. BACPHLIP temperate score 0.11488212098404647 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539635 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 55.1971 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_4998_length_26861_cov_33.150314 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.55 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_4998_length_26861_cov_33.150314 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738665_virus.4998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141603 SAMEA13539636 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738665. BACPHLIP temperate score 0.09741189427312776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539636 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 22.5738 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_5677_length_23829_cov_13.481138 Viral contig found in MAG ERR7738665_bin.299 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_5677_length_23829_cov_13.481138 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0277841 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141604 SAMEA13539637 2133760 Siphoviridae environmental samples This sample represents an uncultured Microcystis phage MaAM05 virus assembled from ERR7738665. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539637 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 216.667 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_835_length_101059_cov_128.793498 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_835_length_101059_cov_128.793498 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME017739 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Victivallales;f__UBA1829;g__UBA11452;s__UBA11452 sp003526375 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738665_virus.835 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Microcystis phage MaAM05 virus enrichment approach none ERS11141605 SAMEA13539638 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738665. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539638 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 45.2589 MAG coverage software Reads (ERR7738665) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Pilot_MoBio_Fiber_I_11_1003__NODE_961_length_92955_cov_26.900138 Viral contig found in MAG ERR7738665_bin.244 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9384027 sample name Pilot_MoBio_Fiber_I_11_1003__NODE_961_length_92955_cov_26.900138 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141606 SAMEA13539639 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738936. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539639 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 6.63249 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1732_length_41801_cov_3.538563_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1732_length_41801_cov_3.538563_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_provirus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141607 SAMEA13539640 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738936. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539640 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 145.009 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_480_length_89518_cov_83.049183_1 Viral contig found in MAG ERR7738936_bin.62 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_480_length_89518_cov_83.049183_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_virus.288 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141608 SAMEA13539641 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738936. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539641 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 14.21 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_800_length_68039_cov_8.156264_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_800_length_68039_cov_8.156264_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.775 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141609 SAMEA13539642 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.03358896201113708 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539642 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 648.36 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 131 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1123_length_56092_cov_412.690262 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1123_length_56092_cov_412.690262 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.1537 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141610 SAMEA13539643 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539643 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 100.467 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 268 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1502_length_46489_cov_57.357645 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4230769230769231 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1502_length_46489_cov_57.357645 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.1285 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141611 SAMEA13539644 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738936. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539644 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 8.51927 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 68 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1844_length_40170_cov_4.927768 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_1844_length_40170_cov_4.927768 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.1844 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141612 SAMEA13539645 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.16497797356828195 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539645 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 14.3319 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 93 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_2012_length_37999_cov_8.553267 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_2012_length_37999_cov_8.553267 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.2012 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141613 SAMEA13539646 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.01110955218654152 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539646 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 10.3677 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_2303_length_34932_cov_5.979142 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_2303_length_34932_cov_5.979142 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.2303 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141614 SAMEA13539647 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539647 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 15.9874 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_2592_length_32198_cov_9.016967 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_2592_length_32198_cov_9.016967 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.2185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141615 SAMEA13539648 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.07047260194774403 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539648 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 31.0052 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_3617_length_25374_cov_17.823932 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_3617_length_25374_cov_17.823932 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_virus.2347 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141616 SAMEA13539649 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539649 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 7.40776 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_4207_length_22668_cov_4.112965 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_4207_length_22668_cov_4.112965 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738561_bin.41 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__UBA1191 sp900066305 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.4207 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141617 SAMEA13539650 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539650 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 18.0725 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_55_length_212516_cov_11.165426 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 86.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 16 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.5471698113207547 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_55_length_212516_cov_11.165426 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__RUG410;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.59 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141618 SAMEA13539651 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738936. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539651 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 63.8955 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_7258_length_15082_cov_38.048117 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_7258_length_15082_cov_38.048117 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000493 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea;s__Dorea formicigenerans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.7258 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141619 SAMEA13539652 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738936. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539652 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 13.9919 MAG coverage software Reads (ERR7738936) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560332) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_G_19_1739__NODE_850_length_66179_cov_8.026202 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585982 sample name Hadza_MoBio_hadza-E-H_G_19_1739__NODE_850_length_66179_cov_8.026202 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747782_bin.309 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus;s__Duodenibacillus sp900544255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.850 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141620 SAMEA13539653 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738937. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539653 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 15.5552 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_1047_length_74371_cov_8.903465_1 Viral contig found in MAG ERR7738937_bin.210 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_1047_length_74371_cov_8.903465_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000662 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7182;s__UBA7182 sp003480725 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738937_provirus.1047 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141621 SAMEA13539654 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738937. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539654 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 72.6157 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 180 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_1290_length_63374_cov_42.468190_1 Viral contig found in MAG ERR7738937_bin.190 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_1290_length_63374_cov_42.468190_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253778 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp003491505 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_provirus.475 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141622 SAMEA13539655 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738937. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539655 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 66.266 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 104 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_272_length_157166_cov_38.515491_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_272_length_157166_cov_38.515491_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__Bilophila wadsworthia vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_provirus.1840 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141623 SAMEA13539656 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738937. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539656 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 169.389 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 374 Number of CRISPR spacer hits supporting host taxonomy 250 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_48_length_323305_cov_97.463441_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.978021978021978 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_48_length_323305_cov_97.463441_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0371292 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141624 SAMEA13539657 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738937. BACPHLIP temperate score 8.6317135549872e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539657 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 83.396 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_878_length_83818_cov_48.675619_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_878_length_83818_cov_48.675619_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375;s__UMGS1375 sp900066615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_provirus.623 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141625 SAMEA13539658 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738937. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539658 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 26.7202 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 90 Number of CRISPR spacer hits supporting host taxonomy 1122 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_1797_length_47890_cov_15.670069 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6944444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_1797_length_47890_cov_15.670069 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141626 SAMEA13539659 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738937. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539659 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 31.7209 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 92 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_2060_length_42982_cov_18.326023 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_2060_length_42982_cov_18.326023 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738276_virus.1589 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141627 SAMEA13539660 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738937. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539660 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 46.9909 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_2490_length_36605_cov_27.509335 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_2490_length_36605_cov_27.509335 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0251436 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141628 SAMEA13539661 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738937. BACPHLIP temperate score 0.17433920704845826 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539661 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 14.4089 MAG coverage software Reads (ERR7738937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Pilot_MoBio_Fiber_L_20_7018__NODE_4339_length_21592_cov_8.693098 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2017 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) USA geographic location (elevation) 29 geographic location (latitude) 37.4275 geographic location (longitude) -122.1697 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1016/j.cell.2021.06.019 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1016/j.cell.2021.06.019 sample collection device or method https://doi.org/10.1016/j.cell.2021.06.019 sample derived from SRS9383899 sample name Pilot_MoBio_Fiber_L_20_7018__NODE_4339_length_21592_cov_8.693098 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738937_virus.4339 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141629 SAMEA13539662 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738938. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539662 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 8.17695 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1144_length_50566_cov_4.247658_1 Viral contig found in MAG ERR7738938_bin.63 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1144_length_50566_cov_4.247658_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_provirus.1144 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141630 SAMEA13539663 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus provirus assembled from ERR7738938. BACPHLIP temperate score 0.06557860569609461 ENA-FIRST-PUBLIC 2022-12-27T01:22:53Z ENA-LAST-UPDATE 2022-12-27T01:22:53Z External Id SAMEA13539663 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 8.05502 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_3443_length_21852_cov_4.273203_1 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_3443_length_21852_cov_4.273203_1 scientific_name Siphoviridae environmental samples sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_provirus.3443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus ERS11141631 SAMEA13539664 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738938. BACPHLIP temperate score 0.03997797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539664 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 48.1415 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_930_length_57738_cov_30.729644_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_930_length_57738_cov_30.729644_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141632 SAMEA13539665 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738938. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539665 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 225.438 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1384_length_43976_cov_129.139320 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1384_length_43976_cov_129.139320 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.1384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141633 SAMEA13539666 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738938. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539666 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 19.014 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1576_length_40278_cov_10.662745 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1576_length_40278_cov_10.662745 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__CAG-238;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.1576 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141634 SAMEA13539667 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738938. BACPHLIP temperate score 0.25243631530483024 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539667 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 11.1656 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1623_length_39422_cov_6.228771 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1623_length_39422_cov_6.228771 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.1623 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141635 SAMEA13539668 2133760 Siphoviridae environmental samples This sample represents an uncultured Enterococcus phage EF5 virus assembled from ERR7738938. BACPHLIP temperate score 0.04343334073279702 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539668 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 80.4655 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_179_length_139821_cov_46.192581 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 13 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.9294871794871796 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_179_length_139821_cov_46.192581 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.179 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Enterococcus phage EF5 virus enrichment approach none ERS11141636 SAMEA13539669 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738938. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539669 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 10.9822 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_202_length_131027_cov_6.033501 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 17 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.43243243243243246 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_202_length_131027_cov_6.033501 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_virus.81 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141637 SAMEA13539670 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738938. BACPHLIP temperate score 0.30247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539670 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 39.9024 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 138 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_2519_length_28472_cov_23.288678 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_2519_length_28472_cov_23.288678 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141638 SAMEA13539671 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738938. BACPHLIP temperate score 0.06442731277533043 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539671 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 9.7257 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 1154 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_2847_length_25622_cov_5.280211 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_2847_length_25622_cov_5.280211 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.1842 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141639 SAMEA13539672 2133760 Siphoviridae environmental samples This sample represents an uncultured Clostridium phage vB_CpeS-1181 virus assembled from ERR7738938. BACPHLIP temperate score 0.08986784140969165 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539672 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 14.4749 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_3497_length_21559_cov_8.037147 Viral contig found in MAG ERR7738938_bin.164 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_3497_length_21559_cov_8.037147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142391 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P perfringens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.3497 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Clostridium phage vB_CpeS-1181 virus enrichment approach none ERS11141640 SAMEA13539673 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7738938. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539673 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 8.38586 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_404_length_91872_cov_4.455537 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.8205128205128205 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_404_length_91872_cov_4.455537 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372168 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141641 SAMEA13539674 2133760 Siphoviridae environmental samples This sample represents an uncultured Maenadvirus virus assembled from ERR7738938. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539674 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 227.448 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_598_length_73945_cov_129.966291 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.845360824742268 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_598_length_73945_cov_129.966291 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738260_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus;s__Lactiplantibacillus plantarum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738277_virus.252 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Tybeckvirinae; Maenadvirus virus enrichment approach none ERS11141642 SAMEA13539675 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738938. BACPHLIP temperate score 0.05236784140969162 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539675 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 226.918 MAG coverage software Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_921_length_57940_cov_130.426715 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787336 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_921_length_57940_cov_130.426715 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738938_virus.921 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141643 SAMEA13539676 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738957. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539676 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 52.8004 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_149_length_161677_cov_33.858676_1 Viral contig found in MAG ERR7738957_bin.118 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_149_length_161677_cov_33.858676_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745625_provirus.431 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141644 SAMEA13539677 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738957. BACPHLIP temperate score 0.5125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539677 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 14.8795 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_2196_length_41925_cov_9.357556_1 Viral contig found in MAG ERR7738957_bin.360 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9130434782608696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_2196_length_41925_cov_9.357556_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_provirus.1362 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141645 SAMEA13539678 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7738957. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539678 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 20.7209 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_332_length_114927_cov_12.889273_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.4230769230769231 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_332_length_114927_cov_12.889273_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738186_provirus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141646 SAMEA13539679 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738957. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539679 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 57.7221 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 96 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_60_length_225080_cov_36.183389_1 Viral contig found in MAG ERR7738957_bin.231 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_60_length_225080_cov_36.183389_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141647 SAMEA13539680 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738957. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539680 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 40.6912 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_914_length_69922_cov_23.922600_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_914_length_69922_cov_23.922600_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738575_bin.23 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-279;s__CAG-279 sp000437795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.557 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141648 SAMEA13539681 336724 Myoviridae environmental samples This sample represents an uncultured unclassified Krischvirus virus assembled from ERR7738957. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539681 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 35.5433 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_133_length_170505_cov_20.882625 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6346863468634686 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_133_length_170505_cov_20.882625 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_virus.84 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae; Krischvirus; unclassified Krischvirus virus enrichment approach none ERS11141649 SAMEA13539682 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738957. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539682 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 43.864 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_1633_length_50948_cov_27.241395 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_1633_length_50948_cov_27.241395 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.1633 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141650 SAMEA13539683 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738957. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539683 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 120.098 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 186 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_1917_length_46025_cov_76.011665 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_1917_length_46025_cov_76.011665 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_virus.884 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141651 SAMEA13539684 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738957. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539684 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 14.228 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_2397_length_39787_cov_8.950844 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.82 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_2397_length_39787_cov_8.950844 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME232176 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter;s__Enterobacter hormaechei_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.2397 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141652 SAMEA13539685 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738957. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539685 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 24.5631 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 115 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_2888_length_35207_cov_14.901139 Viral contig found in MAG ERR7738957_bin.175 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; HMM-based (lower-bound) completeness score 67.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_2888_length_35207_cov_14.901139 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1382 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141653 SAMEA13539686 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738957. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539686 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 17.3201 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 118 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_371_length_109145_cov_11.023279 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; HMM-based (lower-bound) completeness score 94.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_371_length_109145_cov_11.023279 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME276106 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900548615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.371 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141654 SAMEA13539687 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738957. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539687 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 36.2005 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_4647_length_25116_cov_23.871441 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_4647_length_25116_cov_23.871441 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746365_bin.336 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_provirus.3444 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141655 SAMEA13539688 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738957. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539688 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 9.39864 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_5936_length_20800_cov_5.659123 Viral contig found in MAG ERR7738957_bin.309 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_5936_length_20800_cov_5.659123 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096193 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;s__Mediterraneibacter torques vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_virus.2867 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141656 SAMEA13539689 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738957. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539689 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 8.96363 MAG coverage software Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_F_2_1628__NODE_8959_length_15244_cov_5.360094 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585872 sample name Hadza_MoBio_hadza-A-D_F_2_1628__NODE_8959_length_15244_cov_5.360094 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145985 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.8959 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141657 SAMEA13539690 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738959. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539690 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 37.9048 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_119_length_211621_cov_22.881519_1_1 Viral contig found in MAG ERR7738959_bin.83 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_119_length_211621_cov_22.881519_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738241_bin.90 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737;s__UBA737 sp900549055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_provirus.119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141658 SAMEA13539691 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738959. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539691 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 31.9715 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 124 Number of CRISPR spacer hits supporting host taxonomy 160 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_176_length_182345_cov_19.061700_1 Viral contig found in MAG ERR7738959_bin.368 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_176_length_182345_cov_19.061700_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_provirus.176 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141659 SAMEA13539692 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7738959. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539692 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 67.0137 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_24_length_385624_cov_38.964106_1 Viral contig found in MAG ERR7738959_bin.241 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9142857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_24_length_385624_cov_38.964106_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.2420 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141660 SAMEA13539693 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738959. BACPHLIP temperate score 0.095911314301079 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539693 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 16.4446 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_288_length_143254_cov_9.553560_1 Viral contig found in MAG ERR7738959_bin.254 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5757575757575758 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_288_length_143254_cov_9.553560_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_provirus.288 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141661 SAMEA13539694 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7738959. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539694 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 135.866 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_396_length_124280_cov_89.101946_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.9302325581395348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_396_length_124280_cov_89.101946_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738232_provirus.208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141662 SAMEA13539695 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7738959. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539695 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 27.0227 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 162 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_537_length_109571_cov_15.613760_1 Viral contig found in MAG ERR7738959_bin.371 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; HMM-based (lower-bound) completeness score 74.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3157894736842105 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_537_length_109571_cov_15.613760_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096004 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__Desulfovibrio piger vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_provirus.537 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141663 SAMEA13539696 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7738959. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539696 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 184.309 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 100 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_884_length_85684_cov_110.276671_1 Viral contig found in MAG ERR7738959_bin.128 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5806451612903226 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_884_length_85684_cov_110.276671_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738186_provirus.543 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141664 SAMEA13539697 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.0322136563876652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539697 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 12.273 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 96 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_12161_length_13440_cov_6.923356 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_12161_length_13440_cov_6.923356 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.12161 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141665 SAMEA13539698 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539698 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 45.4402 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_16291_length_10493_cov_26.432604 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_16291_length_10493_cov_26.432604 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.4536 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11141666 SAMEA13539699 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539699 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 176.516 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 68 Number of CRISPR spacer hits supporting host taxonomy 112 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_2105_length_50724_cov_103.975576 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_2105_length_50724_cov_103.975576 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141667 SAMEA13539700 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7738959. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539700 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 9.51484 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_2423_length_46687_cov_5.361982 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_2423_length_46687_cov_5.361982 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.2423 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141668 SAMEA13539701 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539701 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 16.3213 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_2740_length_43158_cov_9.779392 Viral contig found in MAG ERR7738959_bin.410 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_2740_length_43158_cov_9.779392 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738556_virus.1073 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141669 SAMEA13539702 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.02349942002795121 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539702 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 50.0205 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_3134_length_38896_cov_28.214225 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_3134_length_38896_cov_28.214225 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141670 SAMEA13539703 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539703 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 7.99232 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 1486 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_3398_length_36716_cov_4.340703 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6451612903225806 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_3398_length_36716_cov_4.340703 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738147_virus.575 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141671 SAMEA13539704 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539704 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 11.8329 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 184 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_3631_length_35130_cov_6.705731 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_3631_length_35130_cov_6.705731 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125893 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger formicilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0250587 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141672 SAMEA13539705 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738959. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539705 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 45.4793 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 143 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_4029_length_32700_cov_26.499770 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_4029_length_32700_cov_26.499770 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.4029 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141673 SAMEA13539706 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539706 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 8.39494 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 133 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_5241_length_26706_cov_4.469263 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_5241_length_26706_cov_4.469263 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1308 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141674 SAMEA13539707 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7738959. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539707 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 257.112 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 341 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_717_length_95550_cov_150.277230 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_717_length_95550_cov_150.277230 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_virus.203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141675 SAMEA13539708 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7738959. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539708 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 17.1231 MAG coverage software Reads (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-E-H_D_4_2182__NODE_9929_length_15877_cov_9.796853 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586147 sample name Hadza_MoBio_hadza-E-H_D_4_2182__NODE_9929_length_15877_cov_9.796853 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738959_virus.9929 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141676 SAMEA13539709 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7739005. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539709 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 16.5774 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_1779_length_60881_cov_9.184050_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_1779_length_60881_cov_9.184050_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_provirus.1779 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141677 SAMEA13539710 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7739005. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539710 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 33.4447 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 237 Number of CRISPR spacer hits supporting host taxonomy 209 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_227_length_197985_cov_19.170094_1 Viral contig found in MAG ERR7739005_bin.144 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.942528735632184 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_227_length_197985_cov_19.170094_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_provirus.227 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141678 SAMEA13539711 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7739005. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539711 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 11.2382 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 378 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_3188_length_37856_cov_6.200005_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_3188_length_37856_cov_6.200005_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253778 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp003491505 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_provirus.475 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141679 SAMEA13539712 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7739005. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539712 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 11.9766 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_479_length_143343_cov_6.570617_1 Viral contig found in MAG ERR7739005_bin.193 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7941176470588235 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_479_length_143343_cov_6.570617_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_provirus.479 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141680 SAMEA13539713 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7739005. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539713 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 37.4067 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 153 Number of CRISPR spacer hits supporting host taxonomy 277 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_9_length_650101_cov_21.520945_1 Viral contig found in MAG ERR7739005_bin.27 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_9_length_650101_cov_21.520945_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp003514385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141681 SAMEA13539714 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7739005. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539714 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 102.212 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_1754_length_61559_cov_58.549624 Viral contig found in MAG ERR7739005_bin.195 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 12 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.4878048780487805 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_1754_length_61559_cov_58.549624 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.815 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141682 SAMEA13539715 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7739005. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539715 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 9.99235 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_2297_length_49535_cov_5.397266 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_2297_length_49535_cov_5.397266 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_virus.2297 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141683 SAMEA13539716 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7739005. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539716 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 28.6822 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_3170_length_38074_cov_16.210174 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_3170_length_38074_cov_16.210174 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_virus.3170 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141684 SAMEA13539717 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7739005. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539717 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 12.2053 MAG coverage software Reads (ERR7739005) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_5139_length_23865_cov_6.695309 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787375 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_1_RAJ0018YZ__NODE_5139_length_23865_cov_6.695309 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025308 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7739005_virus.5139 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141685 SAMEA13539718 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7745291. BACPHLIP temperate score 0.06321814991225902 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539718 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 53.0724 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1079_length_82910_cov_34.934326_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1079_length_82910_cov_34.934326_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_provirus.810 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141686 SAMEA13539719 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745291. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539719 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 59.5674 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1394_length_70983_cov_36.010930_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7027027027027027 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1394_length_70983_cov_36.010930_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFFH01;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_provirus.1394 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141687 SAMEA13539720 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7745291. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539720 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 26.3854 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_2483_length_48773_cov_15.898903_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_2483_length_48773_cov_15.898903_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745787_bin.221 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_provirus.2483 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141688 SAMEA13539721 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745291. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539721 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 16.721800000000002 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_4875_length_29672_cov_10.155736_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_4875_length_29672_cov_10.155736_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.1495 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141689 SAMEA13539722 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745291. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539722 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 251.368 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1046 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_94_length_237268_cov_151.428461_1 Viral contig found in MAG ERR7745291_bin.217 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 78.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_94_length_237268_cov_151.428461_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738575_bin.23 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-279;s__CAG-279 sp000437795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737972_virus.307 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141690 SAMEA13539723 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.06551074844800975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539723 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 12.4187 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1119_length_81190_cov_7.479898 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1119_length_81190_cov_7.479898 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738169_virus.149 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141691 SAMEA13539724 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539724 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 112.732 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1606_length_64900_cov_68.710581 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_1606_length_64900_cov_68.710581 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.1606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141692 SAMEA13539725 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539725 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 8.68811 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_2351_length_50603_cov_5.203796 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_2351_length_50603_cov_5.203796 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.2351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141693 SAMEA13539726 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539726 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 108.664 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_2731_length_45627_cov_65.351745 Viral contig found in MAG ERR7745291_bin.276 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_2731_length_45627_cov_65.351745 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.2731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141694 SAMEA13539727 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 virus assembled from ERR7745291. BACPHLIP temperate score 4.9472295514511e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539727 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:53Z INSDC last update 2022-12-27T01:22:53Z INSDC status public MAG coverage depth 68.5104 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3069_length_42127_cov_41.551201 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3069_length_42127_cov_41.551201 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.997 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11141695 SAMEA13539728 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539728 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 15.4549 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 789 Number of CRISPR spacer hits supporting host taxonomy 1056 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3243_length_40627_cov_9.303329 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7575757575757576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3243_length_40627_cov_9.303329 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_provirus.67 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141696 SAMEA13539729 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539729 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 168.487 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3578_length_37775_cov_108.799326 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3578_length_37775_cov_108.799326 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.3578 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141697 SAMEA13539730 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539730 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 19.9465 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3948_length_35066_cov_12.132442 Viral contig found in MAG ERR7745291_bin.435 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_3948_length_35066_cov_12.132442 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.3948 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141698 SAMEA13539731 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539731 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 15.652 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_4575_length_31213_cov_9.200186 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_4575_length_31213_cov_9.200186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME006546 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-605;s__CAG-605 sp000433255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.165 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141699 SAMEA13539732 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745291. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539732 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 58.0914 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_542_length_119110_cov_35.303328 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_542_length_119110_cov_35.303328 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372834 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141700 SAMEA13539733 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.1437523586468131 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13539733 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-28T19:46:18Z INSDC status public MAG coverage depth 21.198 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_6810_length_22929_cov_13.112813 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_6810_length_22929_cov_13.112813 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.6810 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141701 SAMEA13539734 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745291. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539734 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 20.8324 MAG coverage software Reads (ERR7745291) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559329) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_O_11_2507__NODE_82_length_256725_cov_12.856936 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.55 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586281 sample name Hadza_MoBio_hadza-I-L_O_11_2507__NODE_82_length_256725_cov_12.856936 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738623_bin.157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.82 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141702 SAMEA13539735 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745329. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539735 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 19.8607 MAG coverage software Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_G_24_2613__NODE_1014_length_43158_cov_11.441006_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586323 sample name Hadza_MoBio_hadza-I-L_G_24_2613__NODE_1014_length_43158_cov_11.441006_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745990_bin.52 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548195 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746738_virus.625 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141703 SAMEA13539736 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745329. BACPHLIP temperate score 0.15446967015660706 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539736 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 18.6148 MAG coverage software Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_G_24_2613__NODE_2751_length_18422_cov_10.351213_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586323 sample name Hadza_MoBio_hadza-I-L_G_24_2613__NODE_2751_length_18422_cov_10.351213_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738582_virus.3646 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141704 SAMEA13539737 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745329. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539737 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 14.3092 MAG coverage software Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-I-L_G_24_2613__NODE_690_length_57046_cov_7.944970_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586323 sample name Hadza_MoBio_hadza-I-L_G_24_2613__NODE_690_length_57046_cov_7.944970_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745329_provirus.690 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141705 SAMEA13539738 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745329. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539738 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 50.8379 MAG coverage software Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_G_24_2613__NODE_1258_length_36100_cov_28.126058 Viral contig found in MAG ERR7745329_bin.110 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586323 sample name Hadza_MoBio_hadza-I-L_G_24_2613__NODE_1258_length_36100_cov_28.126058 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME273237 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000;s__CAG-1000 sp000434555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.2705 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141706 SAMEA13539739 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7745329. BACPHLIP temperate score 0.09923314058977054 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539739 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 7.19282 MAG coverage software Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_G_24_2613__NODE_19518_length_3438_cov_4.128236 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586323 sample name Hadza_MoBio_hadza-I-L_G_24_2613__NODE_19518_length_3438_cov_4.128236 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745329_virus.19518 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11141707 SAMEA13539740 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745329. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539740 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 32.9786 MAG coverage software Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 162 Submitter Id Hadza_MoBio_hadza-I-L_G_24_2613__NODE_549_length_66134_cov_18.655358 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586323 sample name Hadza_MoBio_hadza-I-L_G_24_2613__NODE_549_length_66134_cov_18.655358 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745329_virus.549 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141708 SAMEA13539741 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 virus assembled from ERR7745329. BACPHLIP temperate score 0.0286756314816957 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539741 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 9.78533 MAG coverage software Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-I-L_G_24_2613__NODE_951_length_45167_cov_5.368286 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7804878048780488 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586323 sample name Hadza_MoBio_hadza-I-L_G_24_2613__NODE_951_length_45167_cov_5.368286 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738609_virus.1545 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11141709 SAMEA13539742 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745335. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539742 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 11.7868 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_1544_length_67493_cov_6.755444_1 Viral contig found in MAG ERR7745335_bin.408 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_1544_length_67493_cov_6.755444_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.3224 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141710 SAMEA13539743 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745335. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539743 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 12.3525 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_2103_length_56213_cov_7.376870_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_2103_length_56213_cov_7.376870_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_provirus.2103 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141711 SAMEA13539744 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7745335. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539744 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 25.602 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 399 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3_length_665699_cov_15.034449_1 Viral contig found in MAG ERR7745335_bin.290 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7258064516129032 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3_length_665699_cov_15.034449_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_provirus.3 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141712 SAMEA13539745 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745335. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539745 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 334.519 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_428_length_133685_cov_195.891361_1 Viral contig found in MAG ERR7745335_bin.12 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_428_length_133685_cov_195.891361_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_provirus.428 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141713 SAMEA13539746 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745335. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539746 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 95.8359 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_871_length_92958_cov_55.636556_1 Viral contig found in MAG ERR7745335_bin.518 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_871_length_92958_cov_55.636556_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747083_virus.1678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141714 SAMEA13539747 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745335. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539747 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 14.3167 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_12396_length_15277_cov_8.137763 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_12396_length_15277_cov_8.137763 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.12396 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141715 SAMEA13539748 336724 Myoviridae environmental samples This sample represents an uncultured Bacillus virus BCD7 virus assembled from ERR7745335. BACPHLIP temperate score 0.01734581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539748 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 7.84211 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_1821_length_61376_cov_4.260983 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 16 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.23809523809523808 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_1821_length_61376_cov_4.260983 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738627_virus.363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Becedseptimavirus; Bacillus virus BCD7 virus enrichment approach none ERS11141716 SAMEA13539749 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7745335. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539749 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 62.6338 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 108 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_2182_length_54955_cov_36.284486 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_2182_length_54955_cov_36.284486 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME099131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000435075 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.2182 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11141717 SAMEA13539750 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745335. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539750 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 47.0651 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_2660_length_48701_cov_29.626954 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_2660_length_48701_cov_29.626954 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.2660 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141718 SAMEA13539751 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7745335. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539751 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 24.4347 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 380 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3007_length_44886_cov_14.283782 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6388888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3007_length_44886_cov_14.283782 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.3007 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141719 SAMEA13539752 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7745335. BACPHLIP temperate score 0.1217791767270203 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539752 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 10.5765 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3388_length_41371_cov_6.072190 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4090909090909091 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3388_length_41371_cov_6.072190 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.3388 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141720 SAMEA13539753 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745335. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539753 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 79.9741 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1457 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3630_length_39655_cov_48.635707 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3630_length_39655_cov_48.635707 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.3630 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141721 SAMEA13539754 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745335. BACPHLIP temperate score 0.05195538818076477 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539754 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 38.7965 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 70 Number of CRISPR spacer hits supporting host taxonomy 96 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3862_length_38084_cov_22.285974 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_3862_length_38084_cov_22.285974 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737966_provirus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141722 SAMEA13539755 336724 Myoviridae environmental samples This sample represents an uncultured Campylobacter phage DA10 virus assembled from ERR7745335. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539755 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 17.1587 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_4095_length_36632_cov_9.690904 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_4095_length_36632_cov_9.690904 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745335_bin.520 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D;s__Campylobacter_D sp900539255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.4095 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Campylobacter phage DA10 virus enrichment approach none ERS11141723 SAMEA13539756 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745335. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539756 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 482.704 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_4506_length_34321_cov_279.269653 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_4506_length_34321_cov_279.269653 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.1216 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141724 SAMEA13539757 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745335. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539757 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 10.2204 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_5242_length_30478_cov_5.799382 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_5242_length_30478_cov_5.799382 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.1858 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141725 SAMEA13539758 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745335. BACPHLIP temperate score 0.15247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539758 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 9.92516 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_6393_length_26152_cov_5.743739 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_6393_length_26152_cov_5.743739 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.6393 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141726 SAMEA13539759 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745335. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539759 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 17.9887 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_7384_length_23145_cov_10.406581 Viral contig found in MAG ERR7745335_bin.358 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_7384_length_23145_cov_10.406581 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.7384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141727 SAMEA13539760 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745335. BACPHLIP temperate score 0.2954877441377306 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539760 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 8.82197 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_8273_length_21208_cov_5.038900 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_8273_length_21208_cov_5.038900 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140265 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia;s__Blautia stercoris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.8273 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141728 SAMEA13539761 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745335. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539761 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 7.80364 MAG coverage software Reads (ERR7745335) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561292) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Hadza_MoBio_hadza-A-D_D_16_1621__NODE_9968_length_18219_cov_4.071988 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-31 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585870 sample name Hadza_MoBio_hadza-A-D_D_16_1621__NODE_9968_length_18219_cov_4.071988 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.9968 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141729 SAMEA13539762 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745346. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13539762 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-28T19:46:19Z INSDC status public MAG coverage depth 160.506 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 213 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_1694_length_71105_cov_97.178507_1 Viral contig found in MAG ERR7745346_bin.174 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_1694_length_71105_cov_97.178507_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746009_virus.831 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141730 SAMEA13539763 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745346. BACPHLIP temperate score 0.02812088060660004 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539763 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 114.641 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 108 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2093_length_59843_cov_70.571412_1 Viral contig found in MAG ERR7745346_bin.277 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 85.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2093_length_59843_cov_70.571412_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_provirus.2093 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141731 SAMEA13539764 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745346. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539764 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 13.9602 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_3208_length_40261_cov_8.386696_1 Viral contig found in MAG ERR7745346_bin.274 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_3208_length_40261_cov_8.386696_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_provirus.3208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141732 SAMEA13539765 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis provirus assembled from ERR7745346. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539765 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 87.271 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_533_length_152189_cov_54.213915_1 Viral contig found in MAG ERR7745346_bin.211 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5272727272727272 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_533_length_152189_cov_54.213915_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_provirus.533 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11141733 SAMEA13539766 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7745346. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539766 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 15.3971 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_891_length_112347_cov_9.466483_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_891_length_112347_cov_9.466483_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME007797 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__CAG-115 sp003531585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_provirus.891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141734 SAMEA13539767 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745346. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539767 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 33.3932 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_157_length_256542_cov_20.406547 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8028169014084507 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_157_length_256542_cov_20.406547 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000247 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter;s__Intestinibacter bartlettii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.157 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141735 SAMEA13539768 2133760 Siphoviridae environmental samples This sample represents an uncultured Clostridium phage phiCp-D virus assembled from ERR7745346. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539768 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 61.2344 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 125 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2130_length_59108_cov_37.312920 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2130_length_59108_cov_37.312920 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142391 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P perfringens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.2130 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Clostridium phage phiCp-D virus enrichment approach none ERS11141736 SAMEA13539769 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745346. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539769 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 17.388 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2624_length_49133_cov_10.481674 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2624_length_49133_cov_10.481674 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.2624 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141737 SAMEA13539770 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7745346. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539770 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 28.3871 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2977_length_43242_cov_18.481293 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5357142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_2977_length_43242_cov_18.481293 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME007974 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp003516765 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.2977 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11141738 SAMEA13539771 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7745346. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539771 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 552.328 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 449 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_3369_length_38317_cov_335.454890 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_3369_length_38317_cov_335.454890 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.3369 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11141739 SAMEA13539772 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745346. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539772 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 44.2902 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 136 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_3656_length_35188_cov_27.066646 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_3656_length_35188_cov_27.066646 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125893 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger formicilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0352455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141740 SAMEA13539773 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745346. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539773 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 13.3854 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_4562_length_28113_cov_7.988657 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_4562_length_28113_cov_7.988657 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.4562 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141741 SAMEA13539774 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745346. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539774 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 9.52423 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 133 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_5338_length_23674_cov_5.556342 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_5338_length_23674_cov_5.556342 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0315825 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141742 SAMEA13539775 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745346. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539775 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 13.6809 MAG coverage software Reads (ERR7745346) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567276) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_5986_length_20899_cov_8.378398 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787381 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_1_RAJ1015YZ__NODE_5986_length_20899_cov_8.378398 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.5986 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141743 SAMEA13539776 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745362. BACPHLIP temperate score 0.05049472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539776 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 12.443 MAG coverage software Reads (ERR7745362) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 111 Submitter Id Hadza_MoBio_hadza-A-D_D_24_1627__NODE_1100_length_25032_cov_8.054057_1 Viral contig found in MAG ERR7745362_bin.29 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585871 sample name Hadza_MoBio_hadza-A-D_D_24_1627__NODE_1100_length_25032_cov_8.054057_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.128 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;s__Catenibacterium sp900764725 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_provirus.657 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141744 SAMEA13539777 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745362. BACPHLIP temperate score 0.01745594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539777 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 29.8357 MAG coverage software Reads (ERR7745362) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_D_24_1627__NODE_623_length_34343_cov_19.817312_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; HMM-based (lower-bound) completeness score 64.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585871 sample name Hadza_MoBio_hadza-A-D_D_24_1627__NODE_623_length_34343_cov_19.817312_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745362_provirus.623 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141745 SAMEA13539778 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745362. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539778 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 99.8845 MAG coverage software Reads (ERR7745362) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2077 Number of CRISPR spacer hits supporting host taxonomy 94 Submitter Id Hadza_MoBio_hadza-A-D_D_24_1627__NODE_260_length_53390_cov_69.173710 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585871 sample name Hadza_MoBio_hadza-A-D_D_24_1627__NODE_260_length_53390_cov_69.173710 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.216 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141746 SAMEA13539779 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745362. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539779 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 62.7148 MAG coverage software Reads (ERR7745362) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 341 Submitter Id Hadza_MoBio_hadza-A-D_D_24_1627__NODE_71_length_95473_cov_41.683310 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585871 sample name Hadza_MoBio_hadza-A-D_D_24_1627__NODE_71_length_95473_cov_41.683310 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_virus.203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141747 SAMEA13539780 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745366. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539780 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 97.1583 MAG coverage software Reads (ERR7745366) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559737) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_P_8_2346__NODE_31_length_151153_cov_58.930121_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_MoBio_hadza-E-H_P_8_2346__NODE_31_length_151153_cov_58.930121_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.267 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3631;s__UBA3631 sp900546275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745366_provirus.31 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141748 SAMEA13539781 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745366. BACPHLIP temperate score 0.21277445863796457 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539781 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 7.75375 MAG coverage software Reads (ERR7745366) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559737) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_8_2346__NODE_1661_length_17770_cov_4.506415 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_MoBio_hadza-E-H_P_8_2346__NODE_1661_length_17770_cov_4.506415 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738563_provirus.198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141749 SAMEA13539782 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745366. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539782 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 93.4605 MAG coverage software Reads (ERR7745366) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559737) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 152 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_P_8_2346__NODE_3605_length_10308_cov_56.165575 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_MoBio_hadza-E-H_P_8_2346__NODE_3605_length_10308_cov_56.165575 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738513_bin.39 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag1;s__Zag1 sp001765415 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_provirus.1534 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141750 SAMEA13539783 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745366. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539783 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 24.6375 MAG coverage software Reads (ERR7745366) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559737) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_8_2346__NODE_56_length_118808_cov_14.492997 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9305555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586216 sample name Hadza_MoBio_hadza-E-H_P_8_2346__NODE_56_length_118808_cov_14.492997 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745366_virus.56 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141751 SAMEA13539784 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745371. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539784 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 12.858 MAG coverage software Reads (ERR7745371) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559796) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_G_19_2444__NODE_341_length_63841_cov_7.724170_1 Viral contig found in MAG ERR7745371_bin.68 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586238 sample name Hadza_MoBio_hadza-I-L_G_19_2444__NODE_341_length_63841_cov_7.724170_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738592_provirus.338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141752 SAMEA13539785 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745371. BACPHLIP temperate score 0.15566732807002084 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539785 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 8.38423 MAG coverage software Reads (ERR7745371) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559796) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_G_19_2444__NODE_1142_length_31545_cov_5.025518 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586238 sample name Hadza_MoBio_hadza-I-L_G_19_2444__NODE_1142_length_31545_cov_5.025518 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738211_virus.394 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141753 SAMEA13539786 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745371. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539786 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 17.696 MAG coverage software Reads (ERR7745371) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559796) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-I-L_G_19_2444__NODE_23_length_189803_cov_10.482538 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586238 sample name Hadza_MoBio_hadza-I-L_G_19_2444__NODE_23_length_189803_cov_10.482538 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.115 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141754 SAMEA13539787 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745371. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539787 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 41.1299 MAG coverage software Reads (ERR7745371) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559796) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 223 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_hadza-I-L_G_19_2444__NODE_580_length_47468_cov_24.333165 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586238 sample name Hadza_MoBio_hadza-I-L_G_19_2444__NODE_580_length_47468_cov_24.333165 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_provirus.117 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141755 SAMEA13539788 2133760 Siphoviridae environmental samples This sample represents an uncultured unclassified Moineauvirus provirus assembled from ERR7745376. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539788 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 16.999 MAG coverage software Reads (ERR7745376) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560592) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_A_17_1704__NODE_124_length_58323_cov_9.946331_1 Viral contig found in MAG ERR7745376_bin.14 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585947 sample name Hadza_MoBio_hadza-E-H_A_17_1704__NODE_124_length_58323_cov_9.946331_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745376_provirus.124 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Moineauvirus; unclassified Moineauvirus virus enrichment approach none ERS11141756 SAMEA13539789 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745376. BACPHLIP temperate score 0.02241189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539789 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 107.324 MAG coverage software Reads (ERR7745376) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560592) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 181 Number of CRISPR spacer hits supporting host taxonomy 131 Submitter Id Hadza_MoBio_hadza-E-H_A_17_1704__NODE_312_length_25000_cov_67.698271 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585947 sample name Hadza_MoBio_hadza-E-H_A_17_1704__NODE_312_length_25000_cov_67.698271 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095938 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737955_virus.323 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141757 SAMEA13539790 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745378. BACPHLIP temperate score 0.06389767615329436 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539790 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 229.852 MAG coverage software Reads (ERR7745378) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560154) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 517 Submitter Id Hadza_MoBio_hadza-E-H_F_2_2205__NODE_151_length_127848_cov_174.697341_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586154 sample name Hadza_MoBio_hadza-E-H_F_2_2205__NODE_151_length_127848_cov_174.697341_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.1424 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141758 SAMEA13539791 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7745378. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539791 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 9.70817 MAG coverage software Reads (ERR7745378) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560154) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_F_2_2205__NODE_421_length_75450_cov_5.529818_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586154 sample name Hadza_MoBio_hadza-E-H_F_2_2205__NODE_421_length_75450_cov_5.529818_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.29 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900554205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745378_provirus.421 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11141759 SAMEA13539792 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745378. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539792 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 40.9998 MAG coverage software Reads (ERR7745378) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560154) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 127 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_F_2_2205__NODE_1063_length_42116_cov_23.460358 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586154 sample name Hadza_MoBio_hadza-E-H_F_2_2205__NODE_1063_length_42116_cov_23.460358 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0331678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141760 SAMEA13539793 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745378. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539793 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 41.8649 MAG coverage software Reads (ERR7745378) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560154) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 110 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_F_2_2205__NODE_1937_length_26694_cov_25.195401 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586154 sample name Hadza_MoBio_hadza-E-H_F_2_2205__NODE_1937_length_26694_cov_25.195401 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_provirus.1712 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141761 SAMEA13539794 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745378. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539794 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:52Z INSDC last update 2022-12-27T01:22:52Z INSDC status public MAG coverage depth 108.269 MAG coverage software Reads (ERR7745378) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560154) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-E-H_F_2_2205__NODE_243_length_103501_cov_60.660098 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 21 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.9387755102040816 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586154 sample name Hadza_MoBio_hadza-E-H_F_2_2205__NODE_243_length_103501_cov_60.660098 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.476 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141762 SAMEA13539795 2100421 uncultured Caudovirales phage This sample represents an uncultured Picovirinae virus assembled from ERR7745378. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539795 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 86.6803 MAG coverage software Reads (ERR7745378) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560154) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_F_2_2205__NODE_3260_length_17600_cov_49.823318 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586154 sample name Hadza_MoBio_hadza-E-H_F_2_2205__NODE_3260_length_17600_cov_49.823318 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095993 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus;s__Bariatricus comes vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745378_virus.3260 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae; Picovirinae virus enrichment approach none ERS11141763 SAMEA13539796 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7745378. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539796 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 15.1375 MAG coverage software Reads (ERR7745378) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560154) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 153 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-E-H_F_2_2205__NODE_725_length_54691_cov_8.786740 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7037037037037037 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586154 sample name Hadza_MoBio_hadza-E-H_F_2_2205__NODE_725_length_54691_cov_8.786740 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_virus.231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11141764 SAMEA13539797 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745382. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27T01:22:51Z ENA-LAST-UPDATE 2022-12-27T01:22:51Z External Id SAMEA13539797 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 40.3155 MAG coverage software Reads (ERR7745382) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 131 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-I-L_E_21_2379__NODE_42_length_214291_cov_23.168719_1 Viral contig found in MAG ERR7745382_bin.78 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_MoBio_hadza-I-L_E_21_2379__NODE_42_length_214291_cov_23.168719_1 scientific_name Siphoviridae environmental samples sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae ERS11141765 SAMEA13539798 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745382. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539798 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 24.5102 MAG coverage software Reads (ERR7745382) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_E_21_2379__NODE_1097_length_38550_cov_14.066878 Viral contig found in MAG ERR7745382_bin.60 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_MoBio_hadza-I-L_E_21_2379__NODE_1097_length_38550_cov_14.066878 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738248_provirus.1198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141766 SAMEA13539799 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745382. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539799 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 9.14455 MAG coverage software Reads (ERR7745382) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 818 Submitter Id Hadza_MoBio_hadza-I-L_E_21_2379__NODE_1416_length_32152_cov_5.232175 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_MoBio_hadza-I-L_E_21_2379__NODE_1416_length_32152_cov_5.232175 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745382_virus.1416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141767 SAMEA13539800 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7745382. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539800 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 89.4088 MAG coverage software Reads (ERR7745382) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_E_21_2379__NODE_217_length_101909_cov_50.937102 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.989010989010989 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_MoBio_hadza-I-L_E_21_2379__NODE_217_length_101909_cov_50.937102 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0369090 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11141768 SAMEA13539801 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745382. BACPHLIP temperate score 0.05290652265258985 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539801 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 9.57305 MAG coverage software Reads (ERR7745382) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_E_21_2379__NODE_549_length_60019_cov_5.518501 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_MoBio_hadza-I-L_E_21_2379__NODE_549_length_60019_cov_5.518501 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738151_bin.225 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter sp900548765 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_provirus.138 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141769 SAMEA13539802 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745382. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539802 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 87.1394 MAG coverage software Reads (ERR7745382) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 666 Submitter Id Hadza_MoBio_hadza-I-L_E_21_2379__NODE_921_length_43410_cov_57.411188 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586231 sample name Hadza_MoBio_hadza-I-L_E_21_2379__NODE_921_length_43410_cov_57.411188 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_provirus.180 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141770 SAMEA13539803 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745383. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539803 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 21.3128 MAG coverage software Reads (ERR7745383) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560118) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_B_22_2177__NODE_313_length_81978_cov_12.157617_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_hadza-E-H_B_22_2177__NODE_313_length_81978_cov_12.157617_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738217_virus.1221 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141771 SAMEA13539804 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745383. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539804 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 45.5152 MAG coverage software Reads (ERR7745383) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560118) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-E-H_B_22_2177__NODE_1014_length_39248_cov_27.932807 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_hadza-E-H_B_22_2177__NODE_1014_length_39248_cov_27.932807 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746779_virus.1100 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141772 SAMEA13539805 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745383. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539805 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 15.2354 MAG coverage software Reads (ERR7745383) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560118) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 112 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-E-H_B_22_2177__NODE_1447_length_31265_cov_8.853085 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; HMM-based (lower-bound) completeness score 59.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_hadza-E-H_B_22_2177__NODE_1447_length_31265_cov_8.853085 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1382 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141773 SAMEA13539806 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745383. BACPHLIP temperate score 0.00270137614315428 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539806 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 7.94495 MAG coverage software Reads (ERR7745383) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560118) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 68 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-E-H_B_22_2177__NODE_2314_length_21840_cov_4.344530 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_hadza-E-H_B_22_2177__NODE_2314_length_21840_cov_4.344530 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_provirus.854 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141774 SAMEA13539807 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745383. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539807 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 19.2547 MAG coverage software Reads (ERR7745383) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560118) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-E-H_B_22_2177__NODE_44_length_198446_cov_10.709733 Viral contig found in MAG ERR7745383_bin.59 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5151515151515151 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_hadza-E-H_B_22_2177__NODE_44_length_198446_cov_10.709733 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.44 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141775 SAMEA13539808 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745383. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539808 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 9.52246 MAG coverage software Reads (ERR7745383) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560118) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_B_22_2177__NODE_847_length_43876_cov_5.381333 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-10 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586145 sample name Hadza_MoBio_hadza-E-H_B_22_2177__NODE_847_length_43876_cov_5.381333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.847 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141776 SAMEA13539809 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. provirus assembled from ERR7745384. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539809 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 32.3657 MAG coverage software Reads (ERR7745384) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560192) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Hadza_MoBio_hadza-E-H_F_20_2245__NODE_2087_length_26347_cov_24.081043_1_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586163 sample name Hadza_MoBio_hadza-E-H_F_20_2245__NODE_2087_length_26347_cov_24.081043_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745675_provirus.3468 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11141777 SAMEA13539810 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745384. BACPHLIP temperate score 0.05270140052539582 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539810 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 206.55 MAG coverage software Reads (ERR7745384) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560192) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_F_20_2245__NODE_382_length_81574_cov_119.143183_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586163 sample name Hadza_MoBio_hadza-E-H_F_20_2245__NODE_382_length_81574_cov_119.143183_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.1422 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141778 SAMEA13539811 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745384. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539811 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 12.1042 MAG coverage software Reads (ERR7745384) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560192) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_MoBio_hadza-E-H_F_20_2245__NODE_970_length_46831_cov_6.797237_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586163 sample name Hadza_MoBio_hadza-E-H_F_20_2245__NODE_970_length_46831_cov_6.797237_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745836_virus.193 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141779 SAMEA13539812 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745384. BACPHLIP temperate score 0.0630538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539812 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 10.8848 MAG coverage software Reads (ERR7745384) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560192) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 153 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-E-H_F_20_2245__NODE_1644_length_32133_cov_6.045202 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586163 sample name Hadza_MoBio_hadza-E-H_F_20_2245__NODE_1644_length_32133_cov_6.045202 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_virus.2233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141780 SAMEA13539813 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745384. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539813 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 9.81773 MAG coverage software Reads (ERR7745384) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560192) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 78 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_F_20_2245__NODE_2367_length_23593_cov_5.422904 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586163 sample name Hadza_MoBio_hadza-E-H_F_20_2245__NODE_2367_length_23593_cov_5.422904 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141781 SAMEA13539814 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745384. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539814 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 17.0504 MAG coverage software Reads (ERR7745384) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560192) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_F_20_2245__NODE_4197_length_13110_cov_9.986881 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586163 sample name Hadza_MoBio_hadza-E-H_F_20_2245__NODE_4197_length_13110_cov_9.986881 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001159 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A sp900066145 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745675_virus.4730 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141782 SAMEA13539815 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745384. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539815 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 12.5884 MAG coverage software Reads (ERR7745384) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560192) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-E-H_F_20_2245__NODE_695_length_57932_cov_7.082620 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586163 sample name Hadza_MoBio_hadza-E-H_F_20_2245__NODE_695_length_57932_cov_7.082620 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745675_virus.586 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141783 SAMEA13539816 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745386. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539816 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 25.1087 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 404 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_1571_length_25450_cov_13.976156_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_1571_length_25450_cov_13.976156_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME176098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745386_provirus.1571 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141784 SAMEA13539817 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745386. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539817 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 13.8465 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 338 Number of CRISPR spacer hits supporting host taxonomy 210 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_6_length_298064_cov_7.518694_1 Viral contig found in MAG ERR7745386_bin.2 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_6_length_298064_cov_7.518694_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME150720 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp003526955 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745386_provirus.6 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141785 SAMEA13539818 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745386. BACPHLIP temperate score 0.05495594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539818 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 17.5539 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 149 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_1157_length_31753_cov_19.484878 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_1157_length_31753_cov_19.484878 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745386_virus.1157 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141786 SAMEA13539819 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745386. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539819 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 22.1229 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_161_length_97109_cov_12.672067 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_161_length_97109_cov_12.672067 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738250_virus.128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141787 SAMEA13539820 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745386. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539820 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 28.109 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_29_length_180563_cov_15.669963 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_29_length_180563_cov_15.669963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.212 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia;s__Romboutsia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_virus.87 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141788 SAMEA13539821 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745386. BACPHLIP temperate score 0.02177917672702028 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539821 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 45.4612 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_582_length_50478_cov_25.513264 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_582_length_50478_cov_25.513264 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745386_virus.582 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141789 SAMEA13539822 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7745386. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539822 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 18.9913 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 478 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_818_length_39965_cov_10.744008 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_818_length_39965_cov_10.744008 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745386_virus.818 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141790 SAMEA13539823 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745386. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539823 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 50.2296 MAG coverage software Reads (ERR7745386) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560401) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 273 Submitter Id Hadza_MoBio_hadza-E-H_A_10_1818__NODE_993_length_35362_cov_28.851608 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586018 sample name Hadza_MoBio_hadza-E-H_A_10_1818__NODE_993_length_35362_cov_28.851608 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME176098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745386_virus.993 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141791 SAMEA13539824 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745388. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539824 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 22.8803 MAG coverage software Reads (ERR7745388) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559653) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_N_6_2333__NODE_579_length_65713_cov_13.651015_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586203 sample name Hadza_MoBio_hadza-E-H_N_6_2333__NODE_579_length_65713_cov_13.651015_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746741_bin.80 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;s__RUG572 sp900547945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_provirus.467 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141792 SAMEA13539825 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745388. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539825 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 98.9933 MAG coverage software Reads (ERR7745388) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559653) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_N_6_2333__NODE_1083_length_44385_cov_61.043942 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4411764705882353 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586203 sample name Hadza_MoBio_hadza-E-H_N_6_2333__NODE_1083_length_44385_cov_61.043942 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME090929 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__UMGS1441;s__UMGS1441 sp900551755 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745388_virus.1083 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141793 SAMEA13539826 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745388. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539826 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 17.4376 MAG coverage software Reads (ERR7745388) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559653) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_N_6_2333__NODE_1305_length_39422_cov_10.289922 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586203 sample name Hadza_MoBio_hadza-E-H_N_6_2333__NODE_1305_length_39422_cov_10.289922 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745388_virus.1305 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141794 SAMEA13539827 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745388. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539827 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 7.93148 MAG coverage software Reads (ERR7745388) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559653) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 101 Submitter Id Hadza_MoBio_hadza-E-H_N_6_2333__NODE_2288_length_25163_cov_4.859802 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586203 sample name Hadza_MoBio_hadza-E-H_N_6_2333__NODE_2288_length_25163_cov_4.859802 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141795 SAMEA13539828 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745388. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539828 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 8.89549 MAG coverage software Reads (ERR7745388) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559653) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_N_6_2333__NODE_4576_length_14216_cov_5.019238 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586203 sample name Hadza_MoBio_hadza-E-H_N_6_2333__NODE_4576_length_14216_cov_5.019238 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738205_virus.2854 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141796 SAMEA13539829 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7745388. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539829 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 17.9605 MAG coverage software Reads (ERR7745388) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559653) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 104 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_N_6_2333__NODE_863_length_51376_cov_10.409131 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5813953488372093 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586203 sample name Hadza_MoBio_hadza-E-H_N_6_2333__NODE_863_length_51376_cov_10.409131 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11141797 SAMEA13539830 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745389. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539830 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 93.344 MAG coverage software Reads (ERR7745389) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560206) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 363 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_H_2_2257__NODE_17_length_264379_cov_55.568456_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586166 sample name Hadza_MoBio_hadza-E-H_H_2_2257__NODE_17_length_264379_cov_55.568456_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745922_provirus.43 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141798 SAMEA13539831 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745389. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539831 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 8.71892 MAG coverage software Reads (ERR7745389) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560206) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_MoBio_hadza-E-H_H_2_2257__NODE_385_length_75186_cov_4.818584_1 Viral contig found in MAG ERR7745389_bin.43 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7096774193548387 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586166 sample name Hadza_MoBio_hadza-E-H_H_2_2257__NODE_385_length_75186_cov_4.818584_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_provirus.385 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141799 SAMEA13539832 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745389. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539832 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 32.0632 MAG coverage software Reads (ERR7745389) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560206) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_H_2_2257__NODE_1233_length_38054_cov_18.335124 Viral contig found in MAG ERR7745389_bin.38 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586166 sample name Hadza_MoBio_hadza-E-H_H_2_2257__NODE_1233_length_38054_cov_18.335124 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745922_virus.812 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141800 SAMEA13539833 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745389. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539833 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 17.9642 MAG coverage software Reads (ERR7745389) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560206) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-E-H_H_2_2257__NODE_1885_length_27065_cov_10.432896 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586166 sample name Hadza_MoBio_hadza-E-H_H_2_2257__NODE_1885_length_27065_cov_10.432896 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0307965 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141801 SAMEA13539834 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745389. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539834 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 197.858 MAG coverage software Reads (ERR7745389) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560206) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 203 Submitter Id Hadza_MoBio_hadza-E-H_H_2_2257__NODE_275_length_88846_cov_226.136895 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.5853658536585366 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586166 sample name Hadza_MoBio_hadza-E-H_H_2_2257__NODE_275_length_88846_cov_226.136895 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.292 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141802 SAMEA13539835 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745389. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539835 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 18.2591 MAG coverage software Reads (ERR7745389) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560206) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 214 Submitter Id Hadza_MoBio_hadza-E-H_H_2_2257__NODE_506_length_66205_cov_10.464055 Viral contig found in MAG ERR7745389_bin.8 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586166 sample name Hadza_MoBio_hadza-E-H_H_2_2257__NODE_506_length_66205_cov_10.464055 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738172_virus.230 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141803 SAMEA13539836 1478972 Gokushovirinae environmental samples This sample represents an uncultured Gokushovirus WZ-2015a virus assembled from ERR7745389. BACPHLIP temperate score 0.1051009084400288 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539836 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 7.48467 MAG coverage software Reads (ERR7745389) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560206) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_H_2_2257__NODE_9126_length_5337_cov_4.328897 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586166 sample name Hadza_MoBio_hadza-E-H_H_2_2257__NODE_9126_length_5337_cov_4.328897 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745675_virus.10210 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; unclassified Gokushovirinae; Gokushovirus WZ-2015a virus enrichment approach none ERS11141804 SAMEA13539837 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745397. BACPHLIP temperate score 0.1733640890942851 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539837 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 8.97348 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_288_length_84873_cov_5.213442_1 Viral contig found in MAG ERR7745397_bin.133 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_288_length_84873_cov_5.213442_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745388_virus.661 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141805 SAMEA13539838 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745397. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539838 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 14.5795 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_672_length_50832_cov_8.575884_1 Viral contig found in MAG ERR7745397_bin.218 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_672_length_50832_cov_8.575884_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738213_virus.2248 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141806 SAMEA13539839 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745397. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539839 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 10.8616 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 138 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_1197_length_36068_cov_6.459309 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_1197_length_36068_cov_6.459309 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738213_virus.1684 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141807 SAMEA13539840 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745397. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539840 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 36.979 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_144_length_119613_cov_21.539143 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.927536231884058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_144_length_119613_cov_21.539143 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.232 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141808 SAMEA13539841 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745397. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539841 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 12.2295 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_201_length_101303_cov_7.233813 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; HMM-based (lower-bound) completeness score 52.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_201_length_101303_cov_7.233813 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_virus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141809 SAMEA13539842 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745397. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539842 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 63.2407 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_2621_length_21562_cov_36.857529 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_2621_length_21562_cov_36.857529 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.3505 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141810 SAMEA13539843 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745397. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539843 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 13.808 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_34_length_276192_cov_8.204842 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7424242424242424 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_34_length_276192_cov_8.204842 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745397_virus.34 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141811 SAMEA13539844 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745397. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539844 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 29.4264 MAG coverage software Reads (ERR7745397) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561073) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_D_23_1576__NODE_738_length_47978_cov_17.213002 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585825 sample name Hadza_MoBio_hadza-A-D_D_23_1576__NODE_738_length_47978_cov_17.213002 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738610_bin.152 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745397_virus.738 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141812 SAMEA13539845 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745398. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539845 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 156.424 MAG coverage software Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_L_11_1531__NODE_1173_length_38106_cov_94.518683_1 Viral contig found in MAG ERR7745398_bin.79 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_MoBio_hadza-A-D_L_11_1531__NODE_1173_length_38106_cov_94.518683_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_virus.1626 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141813 SAMEA13539846 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745398. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539846 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 75.3567 MAG coverage software Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-A-D_L_11_1531__NODE_272_length_100107_cov_45.103159_1 Viral contig found in MAG ERR7745398_bin.153 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_MoBio_hadza-A-D_L_11_1531__NODE_272_length_100107_cov_45.103159_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0346320 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141814 SAMEA13539847 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745398. BACPHLIP temperate score 0.21216960352422912 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539847 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 10.7238 MAG coverage software Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_L_11_1531__NODE_935_length_45990_cov_6.270533_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_MoBio_hadza-A-D_L_11_1531__NODE_935_length_45990_cov_6.270533_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746365_bin.336 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_provirus.201 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141815 SAMEA13539848 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745398. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539848 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 10.9863 MAG coverage software Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_L_11_1531__NODE_1422_length_32882_cov_6.333791 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_MoBio_hadza-A-D_L_11_1531__NODE_1422_length_32882_cov_6.333791 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME272760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746436_virus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141816 SAMEA13539849 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745398. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539849 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 18.4434 MAG coverage software Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_L_11_1531__NODE_2777_length_18575_cov_10.825549 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_MoBio_hadza-A-D_L_11_1531__NODE_2777_length_18575_cov_10.825549 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745398_virus.2777 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141817 SAMEA13539850 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745398. BACPHLIP temperate score 0.01996515875021345 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539850 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 22.3692 MAG coverage software Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_L_11_1531__NODE_4168_length_13195_cov_13.356990 Viral contig found in MAG ERR7745398_bin.94 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_MoBio_hadza-A-D_L_11_1531__NODE_4168_length_13195_cov_13.356990 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_virus.5711 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141818 SAMEA13539851 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745398. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539851 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 6.63969 MAG coverage software Reads (ERR7745398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560823) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_L_11_1531__NODE_8958_length_6625_cov_3.841326 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_MoBio_hadza-A-D_L_11_1531__NODE_8958_length_6625_cov_3.841326 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_provirus.13346 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11141819 SAMEA13539852 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745402. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539852 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 9.15998 MAG coverage software Reads (ERR7745402) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559900) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_M_1_2491__NODE_281_length_101844_cov_5.123124_1 Viral contig found in MAG ERR7745402_bin.163 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586265 sample name Hadza_MoBio_hadza-I-L_M_1_2491__NODE_281_length_101844_cov_5.123124_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME233621 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D sp000434695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_provirus.88 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141820 SAMEA13539853 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745402. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539853 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 21.3717 MAG coverage software Reads (ERR7745402) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559900) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 178 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_M_1_2491__NODE_737_length_60182_cov_12.501206_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9722222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586265 sample name Hadza_MoBio_hadza-I-L_M_1_2491__NODE_737_length_60182_cov_12.501206_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.1309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141821 SAMEA13539854 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745402. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539854 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 22.3004 MAG coverage software Reads (ERR7745402) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559900) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 94 Submitter Id Hadza_MoBio_hadza-I-L_M_1_2491__NODE_1211_length_42615_cov_12.986459 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586265 sample name Hadza_MoBio_hadza-I-L_M_1_2491__NODE_1211_length_42615_cov_12.986459 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745410_virus.397 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141822 SAMEA13539855 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745402. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539855 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 11.0629 MAG coverage software Reads (ERR7745402) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559900) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_M_1_2491__NODE_1598_length_34421_cov_6.082926 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586265 sample name Hadza_MoBio_hadza-I-L_M_1_2491__NODE_1598_length_34421_cov_6.082926 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.383 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141823 SAMEA13539856 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745402. BACPHLIP temperate score 0.07823510284733451 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539856 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 11.3089 MAG coverage software Reads (ERR7745402) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559900) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-I-L_M_1_2491__NODE_2710_length_21583_cov_6.482470 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586265 sample name Hadza_MoBio_hadza-I-L_M_1_2491__NODE_2710_length_21583_cov_6.482470 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025308 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.2180 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141824 SAMEA13539857 2100421 uncultured Caudovirales phage This sample represents an uncultured Schitoviridae virus assembled from ERR7745402. BACPHLIP temperate score 0.06303277487972782 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539857 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 38.793 MAG coverage software Reads (ERR7745402) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559900) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 324 Submitter Id Hadza_MoBio_hadza-I-L_M_1_2491__NODE_527_length_73968_cov_22.818462 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586265 sample name Hadza_MoBio_hadza-I-L_M_1_2491__NODE_527_length_73968_cov_22.818462 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738189_virus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Schitoviridae virus enrichment approach none ERS11141825 SAMEA13539858 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745403. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539858 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 50.6361 MAG coverage software Reads (ERR7745403) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559773) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_P_20_2369__NODE_114_length_162122_cov_29.136407_1 Viral contig found in MAG ERR7745403_bin.138 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586230 sample name Hadza_MoBio_hadza-I-L_P_20_2369__NODE_114_length_162122_cov_29.136407_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738938_bin.94 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;s__COE1 sp001916965 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745412_provirus.101 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141826 SAMEA13539859 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7745403. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539859 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:51Z INSDC last update 2022-12-27T01:22:51Z INSDC status public MAG coverage depth 40.6256 MAG coverage software Reads (ERR7745403) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559773) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_P_20_2369__NODE_913_length_42775_cov_24.940630_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586230 sample name Hadza_MoBio_hadza-I-L_P_20_2369__NODE_913_length_42775_cov_24.940630_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME209802 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium sp900539885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745403_provirus.913 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11141827 SAMEA13539860 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745403. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539860 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 23.0183 MAG coverage software Reads (ERR7745403) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559773) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-I-L_P_20_2369__NODE_153_length_138150_cov_13.540417 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586230 sample name Hadza_MoBio_hadza-I-L_P_20_2369__NODE_153_length_138150_cov_13.540417 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745403_virus.153 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141828 SAMEA13539861 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7745403. BACPHLIP temperate score 0.20772215993452803 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539861 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 20.3542 MAG coverage software Reads (ERR7745403) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559773) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_P_20_2369__NODE_3991_length_14210_cov_11.904691 Viral contig found in MAG ERR7745403_bin.19 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586230 sample name Hadza_MoBio_hadza-I-L_P_20_2369__NODE_3991_length_14210_cov_11.904691 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745412_virus.3257 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11141829 SAMEA13539862 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7745403. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539862 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 48.2069 MAG coverage software Reads (ERR7745403) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559773) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 78 Number of CRISPR spacer hits supporting host taxonomy 360 Submitter Id Hadza_MoBio_hadza-I-L_P_20_2369__NODE_656_length_54304_cov_28.100780 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7457627118644068 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586230 sample name Hadza_MoBio_hadza-I-L_P_20_2369__NODE_656_length_54304_cov_28.100780 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_virus.783 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11141830 SAMEA13539863 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7745408. BACPHLIP temperate score 0.14888717346443942 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539863 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 10.5238 MAG coverage software Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 108 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-A-D_B_17_1592__NODE_348_length_87485_cov_5.963825_1 Viral contig found in MAG ERR7745408_bin.64 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585841 sample name Hadza_MoBio_hadza-A-D_B_17_1592__NODE_348_length_87485_cov_5.963825_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_provirus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11141831 SAMEA13539864 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745408. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539864 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 143.846 MAG coverage software Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_B_17_1592__NODE_821_length_52563_cov_81.879053_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585841 sample name Hadza_MoBio_hadza-A-D_B_17_1592__NODE_821_length_52563_cov_81.879053_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.551 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141832 SAMEA13539865 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745408. BACPHLIP temperate score 0.17747797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539865 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 68.4711 MAG coverage software Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_hadza-A-D_B_17_1592__NODE_1130_length_41312_cov_41.073966 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585841 sample name Hadza_MoBio_hadza-A-D_B_17_1592__NODE_1130_length_41312_cov_41.073966 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_provirus.745 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141833 SAMEA13539866 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7745408. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539866 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 12.4899 MAG coverage software Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 139 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-A-D_B_17_1592__NODE_1474_length_34170_cov_7.503094 Viral contig found in MAG ERR7745408_bin.201 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585841 sample name Hadza_MoBio_hadza-A-D_B_17_1592__NODE_1474_length_34170_cov_7.503094 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000434975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_provirus.375 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141834 SAMEA13539867 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745408. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539867 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 9.91259 MAG coverage software Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_B_17_1592__NODE_2512_length_23317_cov_5.623795 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585841 sample name Hadza_MoBio_hadza-A-D_B_17_1592__NODE_2512_length_23317_cov_5.623795 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.2258 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141835 SAMEA13539868 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745408. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539868 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 46.2562 MAG coverage software Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_17_1592__NODE_579_length_64458_cov_26.171262 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585841 sample name Hadza_MoBio_hadza-A-D_B_17_1592__NODE_579_length_64458_cov_26.171262 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.483 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141836 SAMEA13539869 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745408. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539869 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 28.4818 MAG coverage software Reads (ERR7745408) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561111) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-A-D_B_17_1592__NODE_832_length_52172_cov_16.351531 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585841 sample name Hadza_MoBio_hadza-A-D_B_17_1592__NODE_832_length_52172_cov_16.351531 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.799 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141837 SAMEA13539870 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745410. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539870 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 38.6446 MAG coverage software Reads (ERR7745410) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559957) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 87 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-I-L_M_7_2493__NODE_146_length_143571_cov_22.715452_1 Viral contig found in MAG ERR7745410_bin.24 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586267 sample name Hadza_MoBio_hadza-I-L_M_7_2493__NODE_146_length_143571_cov_22.715452_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000434975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.1119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141838 SAMEA13539871 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7745410. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539871 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 25.3515 MAG coverage software Reads (ERR7745410) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559957) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_MoBio_hadza-I-L_M_7_2493__NODE_73_length_189672_cov_14.728015_1 Viral contig found in MAG ERR7745410_bin.155 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48148148148148145 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586267 sample name Hadza_MoBio_hadza-I-L_M_7_2493__NODE_73_length_189672_cov_14.728015_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.1266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11141839 SAMEA13539872 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745410. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539872 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 28.7406 MAG coverage software Reads (ERR7745410) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559957) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-I-L_M_7_2493__NODE_1183_length_41822_cov_16.522554 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586267 sample name Hadza_MoBio_hadza-I-L_M_7_2493__NODE_1183_length_41822_cov_16.522554 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.105 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp900552845 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745410_virus.1183 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141840 SAMEA13539873 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745410. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539873 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 7.96317 MAG coverage software Reads (ERR7745410) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559957) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_M_7_2493__NODE_1847_length_29501_cov_4.344175 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586267 sample name Hadza_MoBio_hadza-I-L_M_7_2493__NODE_1847_length_29501_cov_4.344175 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__MARSEILLE-P3954;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.1568 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141841 SAMEA13539874 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745410. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539874 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 43.0106 MAG coverage software Reads (ERR7745410) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559957) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-I-L_M_7_2493__NODE_396_length_85712_cov_24.914953 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586267 sample name Hadza_MoBio_hadza-I-L_M_7_2493__NODE_396_length_85712_cov_24.914953 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745867_virus.384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141842 SAMEA13539875 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745410. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539875 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 11.6405 MAG coverage software Reads (ERR7745410) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559957) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 479 Submitter Id Hadza_MoBio_hadza-I-L_M_7_2493__NODE_803_length_54712_cov_6.785449 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586267 sample name Hadza_MoBio_hadza-I-L_M_7_2493__NODE_803_length_54712_cov_6.785449 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.907 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141843 SAMEA13539876 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745411. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539876 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 17.6607 MAG coverage software Reads (ERR7745411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 157 Submitter Id Hadza_MoBio_hadza-A-D_J_23_1541__NODE_1042_length_38541_cov_10.718724 Viral contig found in MAG ERR7745411_bin.151 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585795 sample name Hadza_MoBio_hadza-A-D_J_23_1541__NODE_1042_length_38541_cov_10.718724 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745433_virus.963 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141844 SAMEA13539877 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745411. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539877 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 8.92801 MAG coverage software Reads (ERR7745411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-A-D_J_23_1541__NODE_2016_length_21791_cov_5.260017 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585795 sample name Hadza_MoBio_hadza-A-D_J_23_1541__NODE_2016_length_21791_cov_5.260017 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745411_virus.2016 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141845 SAMEA13539878 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745411. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539878 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 12.9018 MAG coverage software Reads (ERR7745411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_J_23_1541__NODE_3610_length_12909_cov_8.214931 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585795 sample name Hadza_MoBio_hadza-A-D_J_23_1541__NODE_3610_length_12909_cov_8.214931 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745411_virus.3610 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141846 SAMEA13539879 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745411. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539879 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 154.625 MAG coverage software Reads (ERR7745411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566898) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_J_23_1541__NODE_76_length_181224_cov_94.207406 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6216216216216216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585795 sample name Hadza_MoBio_hadza-A-D_J_23_1541__NODE_76_length_181224_cov_94.207406 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746692_virus.42 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141847 SAMEA13539880 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745412. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539880 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 59.4083 MAG coverage software Reads (ERR7745412) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559636) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_N_4_2332__NODE_101_length_170703_cov_35.394787_1 Viral contig found in MAG ERR7745412_bin.21 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586202 sample name Hadza_MoBio_hadza-E-H_N_4_2332__NODE_101_length_170703_cov_35.394787_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738938_bin.94 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;s__COE1 sp001916965 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745412_provirus.101 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141848 SAMEA13539881 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745412. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539881 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 82.5274 MAG coverage software Reads (ERR7745412) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559636) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_N_4_2332__NODE_593_length_60110_cov_55.717872_1 Viral contig found in MAG ERR7745412_bin.86 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586202 sample name Hadza_MoBio_hadza-E-H_N_4_2332__NODE_593_length_60110_cov_55.717872_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745412_provirus.593 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141849 SAMEA13539882 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745412. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539882 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 86.9737 MAG coverage software Reads (ERR7745412) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559636) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_N_4_2332__NODE_1232_length_35444_cov_49.790794 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586202 sample name Hadza_MoBio_hadza-E-H_N_4_2332__NODE_1232_length_35444_cov_49.790794 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME134541 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C;s__Ruminococcus_C sp000437255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_virus.1437 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141850 SAMEA13539883 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745412. BACPHLIP temperate score 0.00495594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539883 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 8.38668 MAG coverage software Reads (ERR7745412) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559636) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-E-H_N_4_2332__NODE_2519_length_20490_cov_4.700926 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586202 sample name Hadza_MoBio_hadza-E-H_N_4_2332__NODE_2519_length_20490_cov_4.700926 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0245806 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141851 SAMEA13539884 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745412. BACPHLIP temperate score 0.6274779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539884 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 44.7394 MAG coverage software Reads (ERR7745412) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559636) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 104 Submitter Id Hadza_MoBio_hadza-E-H_N_4_2332__NODE_597_length_59632_cov_25.840803 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586202 sample name Hadza_MoBio_hadza-E-H_N_4_2332__NODE_597_length_59632_cov_25.840803 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738166_provirus.152 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141852 SAMEA13539885 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745414. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539885 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 12.8076 MAG coverage software Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_L_5_1538__NODE_1314_length_37009_cov_7.697633_1 Viral contig found in MAG ERR7745414_bin.26 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585792 sample name Hadza_MoBio_hadza-A-D_L_5_1538__NODE_1314_length_37009_cov_7.697633_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737956_provirus.772 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141853 SAMEA13539886 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis provirus assembled from ERR7745414. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539886 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 26.2763 MAG coverage software Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 92 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_L_5_1538__NODE_488_length_65892_cov_15.532690_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.27450980392156865 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585792 sample name Hadza_MoBio_hadza-A-D_L_5_1538__NODE_488_length_65892_cov_15.532690_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_virus.231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11141854 SAMEA13539887 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745414. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539887 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 27.4333 MAG coverage software Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-A-D_L_5_1538__NODE_1037_length_42378_cov_16.124914 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585792 sample name Hadza_MoBio_hadza-A-D_L_5_1538__NODE_1037_length_42378_cov_16.124914 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.3571512 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141855 SAMEA13539888 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745414. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539888 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 75.0735 MAG coverage software Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 198 Submitter Id Hadza_MoBio_hadza-A-D_L_5_1538__NODE_1381_length_35668_cov_43.874435 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4705882352941176 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585792 sample name Hadza_MoBio_hadza-A-D_L_5_1538__NODE_1381_length_35668_cov_43.874435 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_virus.1280 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141856 SAMEA13539889 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745414. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539889 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 29.0627 MAG coverage software Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_L_5_1538__NODE_2019_length_28135_cov_17.481360 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585792 sample name Hadza_MoBio_hadza-A-D_L_5_1538__NODE_2019_length_28135_cov_17.481360 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.3010 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141857 SAMEA13539890 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7745414. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539890 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 4.079 MAG coverage software Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_L_5_1538__NODE_50498_length_2264_cov_2.257888 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585792 sample name Hadza_MoBio_hadza-A-D_L_5_1538__NODE_50498_length_2264_cov_2.257888 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738664_bin.300 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter sp900543445 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-3219806 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11141858 SAMEA13539891 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745414. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539891 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 13.6366 MAG coverage software Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_L_5_1538__NODE_9555_length_8348_cov_8.284972 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585792 sample name Hadza_MoBio_hadza-A-D_L_5_1538__NODE_9555_length_8348_cov_8.284972 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159485 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_provirus.5185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141859 SAMEA13539892 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745419. BACPHLIP temperate score 0.09955947136563878 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539892 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 13.154 MAG coverage software Reads (ERR7745419) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559960) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 81 Submitter Id Hadza_MoBio_hadza-I-L_O_5_2504__NODE_17_length_292599_cov_7.583300_1_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586278 sample name Hadza_MoBio_hadza-I-L_O_5_2504__NODE_17_length_292599_cov_7.583300_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_provirus.81 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141860 SAMEA13539893 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745419. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539893 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 24.309 MAG coverage software Reads (ERR7745419) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559960) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-I-L_O_5_2504__NODE_756_length_56750_cov_14.417677_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586278 sample name Hadza_MoBio_hadza-I-L_O_5_2504__NODE_756_length_56750_cov_14.417677_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141861 SAMEA13539894 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745419. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539894 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 60.2352 MAG coverage software Reads (ERR7745419) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559960) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 127 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_O_5_2504__NODE_1250_length_41473_cov_36.291115 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586278 sample name Hadza_MoBio_hadza-I-L_O_5_2504__NODE_1250_length_41473_cov_36.291115 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0331678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141862 SAMEA13539895 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745419. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539895 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 7.09168 MAG coverage software Reads (ERR7745419) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559960) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-I-L_O_5_2504__NODE_1708_length_33179_cov_4.010664 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586278 sample name Hadza_MoBio_hadza-I-L_O_5_2504__NODE_1708_length_33179_cov_4.010664 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1382 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141863 SAMEA13539896 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745419. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539896 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 9.97832 MAG coverage software Reads (ERR7745419) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559960) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_O_5_2504__NODE_3282_length_18786_cov_5.870918 Viral contig found in MAG ERR7745419_bin.149 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586278 sample name Hadza_MoBio_hadza-I-L_O_5_2504__NODE_3282_length_18786_cov_5.870918 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746398_bin.161 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;s__Oribacterium sp900772695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.1873 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141864 SAMEA13539897 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745419. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539897 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 11.4022 MAG coverage software Reads (ERR7745419) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559960) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-I-L_O_5_2504__NODE_598_length_64034_cov_6.731460 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586278 sample name Hadza_MoBio_hadza-I-L_O_5_2504__NODE_598_length_64034_cov_6.731460 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738616_bin.92 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745398_virus.207 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141865 SAMEA13539898 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745419. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539898 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 10.1784 MAG coverage software Reads (ERR7745419) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559960) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_O_5_2504__NODE_8808_length_7220_cov_5.900182 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586278 sample name Hadza_MoBio_hadza-I-L_O_5_2504__NODE_8808_length_7220_cov_5.900182 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747782_bin.118 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D berlinense vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745419_virus.8808 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11141866 SAMEA13539899 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745420. BACPHLIP temperate score 0.525 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539899 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 34.1771 MAG coverage software Reads (ERR7745420) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_H_14_2281__NODE_60_length_123945_cov_24.690873_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586172 sample name Hadza_MoBio_hadza-E-H_H_14_2281__NODE_60_length_123945_cov_24.690873_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_provirus.57 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141867 SAMEA13539900 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745420. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539900 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 6.37825 MAG coverage software Reads (ERR7745420) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_H_14_2281__NODE_1382_length_24964_cov_3.291879 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586172 sample name Hadza_MoBio_hadza-E-H_H_14_2281__NODE_1382_length_24964_cov_3.291879 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_virus.884 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141868 SAMEA13539901 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745420. BACPHLIP temperate score 0.4375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539901 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 9.53359 MAG coverage software Reads (ERR7745420) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 305 Submitter Id Hadza_MoBio_hadza-E-H_H_14_2281__NODE_287_length_59297_cov_5.532506 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586172 sample name Hadza_MoBio_hadza-E-H_H_14_2281__NODE_287_length_59297_cov_5.532506 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_virus.391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141869 SAMEA13539902 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745420. BACPHLIP temperate score 0.44441133531732857 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539902 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 66.3785 MAG coverage software Reads (ERR7745420) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_H_14_2281__NODE_584_length_40786_cov_40.394434 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586172 sample name Hadza_MoBio_hadza-E-H_H_14_2281__NODE_584_length_40786_cov_40.394434 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141870 SAMEA13539903 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7745420. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539903 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 197.233 MAG coverage software Reads (ERR7745420) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560258) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 159 Submitter Id Hadza_MoBio_hadza-E-H_H_14_2281__NODE_834_length_33484_cov_122.607597 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586172 sample name Hadza_MoBio_hadza-E-H_H_14_2281__NODE_834_length_33484_cov_122.607597 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745420_virus.834 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141871 SAMEA13539904 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745423. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539904 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 32.931 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_22_length_297370_cov_19.394520_1 Viral contig found in MAG ERR7745423_bin.46 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_22_length_297370_cov_19.394520_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_provirus.22 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141872 SAMEA13539905 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745423. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539905 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 52.9777 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 69 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_659_length_55336_cov_31.017174_1 Viral contig found in MAG ERR7745423_bin.131 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_659_length_55336_cov_31.017174_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__RUG410;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_provirus.659 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141873 SAMEA13539906 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745423. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539906 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 11.5433 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 148 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_1348_length_33690_cov_6.757386 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7741935483870968 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_1348_length_33690_cov_6.757386 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_virus.1348 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141874 SAMEA13539907 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745423. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539907 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 10.2743 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 513 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_1864_length_26268_cov_5.910962 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_1864_length_26268_cov_5.910962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA3388;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746233_virus.201 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141875 SAMEA13539908 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745423. BACPHLIP temperate score 0.11996874984972046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539908 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 12.3078 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_2670_length_20335_cov_6.991164 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_2670_length_20335_cov_6.991164 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141876 SAMEA13539909 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745423. BACPHLIP temperate score 0.7699339207048458 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539909 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 467.991 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 211 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_552_length_61816_cov_272.213010 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_552_length_61816_cov_272.213010 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746233_virus.186 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141877 SAMEA13539910 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745423. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539910 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 17.4772 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_858_length_46015_cov_10.139884 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_858_length_46015_cov_10.139884 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.2134 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141878 SAMEA13539911 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745423. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539911 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 7.80641 MAG coverage software Reads (ERR7745423) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562234) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_F_8_1631__NODE_963_length_42369_cov_4.320841 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585875 sample name Hadza_MoBio_hadza-A-D_F_8_1631__NODE_963_length_42369_cov_4.320841 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_virus.963 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141879 SAMEA13539912 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745425. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539912 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 18.3435 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_164_length_139784_cov_10.543029_1 Viral contig found in MAG ERR7745425_bin.74 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_164_length_139784_cov_10.543029_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738624_bin.279 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAAFZY01;s__CAAFZY01 sp900767645 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745577_provirus.97 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141880 SAMEA13539913 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745425. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539913 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 45.7169 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 82 Number of CRISPR spacer hits supporting host taxonomy 138 Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_63_length_205746_cov_26.626847_1 Viral contig found in MAG ERR7745425_bin.142 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_63_length_205746_cov_26.626847_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_provirus.63 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141881 SAMEA13539914 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745425. BACPHLIP temperate score 0.10082464483052038 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539914 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 97.3946 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_1085_length_44056_cov_56.907683 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_1085_length_44056_cov_56.907683 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.1113 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141882 SAMEA13539915 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745425. BACPHLIP temperate score 0.11497797356828196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539915 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 10.6231 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_1572_length_33900_cov_5.904562 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_1572_length_33900_cov_5.904562 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141883 SAMEA13539916 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745425. BACPHLIP temperate score 0.6875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539916 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 14.1253 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_2253_length_25225_cov_7.905082 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_2253_length_25225_cov_7.905082 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME086861 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter;s__Fusicatenibacter saccharivorans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.3584 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141884 SAMEA13539917 2133760 Siphoviridae environmental samples This sample represents an uncultured Erysipelothrix phage phi1605 virus assembled from ERR7745425. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539917 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 76.6152 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_2674_length_21738_cov_46.522137 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_2674_length_21738_cov_46.522137 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737969_virus.1469 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Erysipelothrix phage phi1605 virus enrichment approach none ERS11141885 SAMEA13539918 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745425. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539918 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 6.05087 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_4190_length_15129_cov_3.326601 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_4190_length_15129_cov_3.326601 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.170 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900768995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.4190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141886 SAMEA13539919 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745425. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539919 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 39.2428 MAG coverage software Reads (ERR7745425) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561787) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_A_12_1112__NODE_757_length_57255_cov_24.163052 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_MoBio_hadza-A-D_A_12_1112__NODE_757_length_57255_cov_24.163052 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.757 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141887 SAMEA13539920 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7745427. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539920 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 258.919 MAG coverage software Reads (ERR7745427) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560244) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 224 Submitter Id Hadza_MoBio_hadza-E-H_F_22_2249__NODE_105_length_155373_cov_266.154447_1 Viral contig found in MAG ERR7745427_bin.159 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4186046511627907 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586164 sample name Hadza_MoBio_hadza-E-H_F_22_2249__NODE_105_length_155373_cov_266.154447_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745427_provirus.105 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141888 SAMEA13539921 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745427. BACPHLIP temperate score 0.01734581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539921 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 65.2873 MAG coverage software Reads (ERR7745427) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560244) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_MoBio_hadza-E-H_F_22_2249__NODE_267_length_105624_cov_37.818697_1 Viral contig found in MAG ERR7745427_bin.104 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586164 sample name Hadza_MoBio_hadza-E-H_F_22_2249__NODE_267_length_105624_cov_37.818697_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141889 SAMEA13539922 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745427. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539922 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 21.2731 MAG coverage software Reads (ERR7745427) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560244) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 348 Submitter Id Hadza_MoBio_hadza-E-H_F_22_2249__NODE_719_length_58478_cov_12.425506_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586164 sample name Hadza_MoBio_hadza-E-H_F_22_2249__NODE_719_length_58478_cov_12.425506_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.1355 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141890 SAMEA13539923 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745427. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539923 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 14.0492 MAG coverage software Reads (ERR7745427) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560244) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_F_22_2249__NODE_114_length_150387_cov_8.067574 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.6206896551724138 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586164 sample name Hadza_MoBio_hadza-E-H_F_22_2249__NODE_114_length_150387_cov_8.067574 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_provirus.155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141891 SAMEA13539924 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745427. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539924 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 60.4339 MAG coverage software Reads (ERR7745427) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560244) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_F_22_2249__NODE_1736_length_32699_cov_36.212004 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586164 sample name Hadza_MoBio_hadza-E-H_F_22_2249__NODE_1736_length_32699_cov_36.212004 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0307965 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141892 SAMEA13539925 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745427. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539925 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 17.49 MAG coverage software Reads (ERR7745427) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560244) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-E-H_F_22_2249__NODE_545_length_69403_cov_10.211551 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 82.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7741935483870968 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586164 sample name Hadza_MoBio_hadza-E-H_F_22_2249__NODE_545_length_69403_cov_10.211551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747426_bin.316 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D succinifaciens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745427_virus.545 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141893 SAMEA13539926 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745429. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539926 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 21.1329 MAG coverage software Reads (ERR7745429) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561281) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 176 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_F_10_1632__NODE_1322_length_27344_cov_12.115818_1 Viral contig found in MAG ERR7745429_bin.125 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585876 sample name Hadza_MoBio_hadza-A-D_F_10_1632__NODE_1322_length_27344_cov_12.115818_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0091843 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141894 SAMEA13539927 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745429. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539927 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 31.0896 MAG coverage software Reads (ERR7745429) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561281) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_F_10_1632__NODE_280_length_79726_cov_18.756846_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585876 sample name Hadza_MoBio_hadza-A-D_F_10_1632__NODE_280_length_79726_cov_18.756846_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738195_bin.52 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738605_provirus.824 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141895 SAMEA13539928 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745429. BACPHLIP temperate score 0.01745594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539928 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 30.7367 MAG coverage software Reads (ERR7745429) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561281) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_F_10_1632__NODE_52_length_164658_cov_18.504177_1 Viral contig found in MAG ERR7745429_bin.149 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585876 sample name Hadza_MoBio_hadza-A-D_F_10_1632__NODE_52_length_164658_cov_18.504177_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738195_bin.52 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745429_provirus.52 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141896 SAMEA13539929 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745429. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539929 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:50Z INSDC last update 2022-12-27T01:22:50Z INSDC status public MAG coverage depth 19.0248 MAG coverage software Reads (ERR7745429) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561281) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_F_10_1632__NODE_1417_length_25876_cov_11.628009 Viral contig found in MAG ERR7745429_bin.57 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9642857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585876 sample name Hadza_MoBio_hadza-A-D_F_10_1632__NODE_1417_length_25876_cov_11.628009 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745429_bin.57 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_G;s__Enterococcus_G italicus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745429_virus.1417 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141897 SAMEA13539930 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745429. BACPHLIP temperate score 0.06798872201629169 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539930 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 15.0402 MAG coverage software Reads (ERR7745429) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561281) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_F_10_1632__NODE_2474_length_17059_cov_8.742551 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585876 sample name Hadza_MoBio_hadza-A-D_F_10_1632__NODE_2474_length_17059_cov_8.742551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745429_virus.2474 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141898 SAMEA13539931 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745429. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539931 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 38.4908 MAG coverage software Reads (ERR7745429) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561281) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 325 Submitter Id Hadza_MoBio_hadza-A-D_F_10_1632__NODE_709_length_42155_cov_22.816959 Viral contig found in MAG ERR7745429_bin.152 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585876 sample name Hadza_MoBio_hadza-A-D_F_10_1632__NODE_709_length_42155_cov_22.816959 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME212098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745429_virus.709 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141899 SAMEA13539932 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745431. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539932 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 12.5463 MAG coverage software Reads (ERR7745431) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561105) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 96 Number of CRISPR spacer hits supporting host taxonomy 80 Submitter Id Hadza_MoBio_C-REDO_F_6_1569__NODE_122_length_149128_cov_7.036075_1 Viral contig found in MAG ERR7745431_bin.19 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585823 sample name Hadza_MoBio_C-REDO_F_6_1569__NODE_122_length_149128_cov_7.036075_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141900 SAMEA13539933 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745431. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539933 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 89.0952 MAG coverage software Reads (ERR7745431) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561105) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 560 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_C-REDO_F_6_1569__NODE_411_length_77864_cov_52.122283_1 Viral contig found in MAG ERR7745431_bin.158 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585823 sample name Hadza_MoBio_C-REDO_F_6_1569__NODE_411_length_77864_cov_52.122283_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745431_provirus.411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141901 SAMEA13539934 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745431. BACPHLIP temperate score 0.19493392070484583 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539934 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 79.2715 MAG coverage software Reads (ERR7745431) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561105) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 407 Submitter Id Hadza_MoBio_C-REDO_F_6_1569__NODE_98_length_164667_cov_45.223792_1 Viral contig found in MAG ERR7745431_bin.158 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585823 sample name Hadza_MoBio_C-REDO_F_6_1569__NODE_98_length_164667_cov_45.223792_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11141902 SAMEA13539935 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745431. BACPHLIP temperate score 0.11543966842021684 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539935 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 11.2077 MAG coverage software Reads (ERR7745431) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561105) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_C-REDO_F_6_1569__NODE_1305_length_35069_cov_6.243627 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585823 sample name Hadza_MoBio_C-REDO_F_6_1569__NODE_1305_length_35069_cov_6.243627 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746436_virus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141903 SAMEA13539936 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7745431. BACPHLIP temperate score 0.12878892628021937 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539936 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 18.1958 MAG coverage software Reads (ERR7745431) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561105) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_C-REDO_F_6_1569__NODE_255_length_98774_cov_10.182640 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585823 sample name Hadza_MoBio_C-REDO_F_6_1569__NODE_255_length_98774_cov_10.182640 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746012_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11141904 SAMEA13539937 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745431. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539937 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 26.6192 MAG coverage software Reads (ERR7745431) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561105) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_F_6_1569__NODE_382_length_80904_cov_15.618296 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585823 sample name Hadza_MoBio_C-REDO_F_6_1569__NODE_382_length_80904_cov_15.618296 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745431_virus.382 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11141905 SAMEA13539938 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745431. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539938 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 9.14898 MAG coverage software Reads (ERR7745431) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561105) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_C-REDO_F_6_1569__NODE_8717_length_6520_cov_5.282011 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585823 sample name Hadza_MoBio_C-REDO_F_6_1569__NODE_8717_length_6520_cov_5.282011 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_provirus.13346 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11141906 SAMEA13539939 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7745432. BACPHLIP temperate score 0.6 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539939 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 18.2761 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_19_length_269136_cov_10.379151_1 Viral contig found in MAG ERR7745432_bin.166 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 73.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_19_length_269136_cov_10.379151_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746741_bin.80 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572;s__RUG572 sp900547945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141907 SAMEA13539940 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745432. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539940 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 69.8374 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_80_length_173611_cov_68.043813_1 Viral contig found in MAG ERR7745432_bin.70 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_80_length_173611_cov_68.043813_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_provirus.80 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141908 SAMEA13539941 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745432. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539941 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 20.0818 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_118_length_146770_cov_11.243631 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7045454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_118_length_146770_cov_11.243631 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141909 SAMEA13539942 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745432. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539942 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 11.2463 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_1475_length_35495_cov_6.278248 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 68.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_1475_length_35495_cov_6.278248 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738622_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141910 SAMEA13539943 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745432. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539943 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 16.0232 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 245 Number of CRISPR spacer hits supporting host taxonomy 129 Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_1921_length_29102_cov_9.319518 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_1921_length_29102_cov_9.319518 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.1890 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141911 SAMEA13539944 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745432. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539944 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 13.4729 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 93 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_2416_length_24218_cov_7.835425 Viral contig found in MAG ERR7745432_bin.158 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_2416_length_24218_cov_7.835425 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0296258 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141912 SAMEA13539945 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus virus assembled from ERR7745432. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539945 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 7.17577 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_4029_length_15528_cov_3.811922 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_4029_length_15528_cov_3.811922 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.4029 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11141913 SAMEA13539946 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745432. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539946 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 238.228 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_614_length_60778_cov_136.139652 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 68.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_614_length_60778_cov_136.139652 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.780 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141914 SAMEA13539947 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7745432. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539947 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 37.0323 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 402 Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_744_length_54621_cov_20.744133 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_744_length_54621_cov_20.744133 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.744 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141915 SAMEA13539948 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745432. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539948 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 26.128 MAG coverage software Reads (ERR7745432) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561552) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_B_20_1162__NODE_845_length_50672_cov_14.304220 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585586 sample name Hadza_MoBio_hadza-I-L_B_20_1162__NODE_845_length_50672_cov_14.304220 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.845 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141916 SAMEA13539949 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745433. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539949 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 363.902 MAG coverage software Reads (ERR7745433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561097) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 93 Submitter Id Hadza_MoBio_hadza-A-D_D_13_1581__NODE_20_length_312805_cov_213.669006_1 Viral contig found in MAG ERR7745433_bin.124 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 44.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4827586206896552 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585830 sample name Hadza_MoBio_hadza-A-D_D_13_1581__NODE_20_length_312805_cov_213.669006_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746692_provirus.15 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141917 SAMEA13539950 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745433. BACPHLIP temperate score 0.29245594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539950 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:49Z INSDC last update 2022-12-27T01:22:49Z INSDC status public MAG coverage depth 10.4273 MAG coverage software Reads (ERR7745433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561097) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-A-D_D_13_1581__NODE_690_length_49299_cov_5.989761_1 Viral contig found in MAG ERR7745433_bin.97 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585830 sample name Hadza_MoBio_hadza-A-D_D_13_1581__NODE_690_length_49299_cov_5.989761_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737972_provirus.947 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141918 SAMEA13539951 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745433. BACPHLIP temperate score 0.05247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539951 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 7.37216 MAG coverage software Reads (ERR7745433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561097) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_D_13_1581__NODE_1739_length_26488_cov_4.269736 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585830 sample name Hadza_MoBio_hadza-A-D_D_13_1581__NODE_1739_length_26488_cov_4.269736 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745433_virus.1739 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141919 SAMEA13539952 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745433. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539952 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 30.2753 MAG coverage software Reads (ERR7745433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561097) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_D_13_1581__NODE_272_length_82574_cov_17.123798 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585830 sample name Hadza_MoBio_hadza-A-D_D_13_1581__NODE_272_length_82574_cov_17.123798 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_virus.379 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141920 SAMEA13539953 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7745433. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539953 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 69.3717 MAG coverage software Reads (ERR7745433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561097) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-A-D_D_13_1581__NODE_537_length_56924_cov_40.835365 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585830 sample name Hadza_MoBio_hadza-A-D_D_13_1581__NODE_537_length_56924_cov_40.835365 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.189 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11141921 SAMEA13539954 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745433. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539954 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 32.8302 MAG coverage software Reads (ERR7745433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561097) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-A-D_D_13_1581__NODE_851_length_43278_cov_19.058494 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585830 sample name Hadza_MoBio_hadza-A-D_D_13_1581__NODE_851_length_43278_cov_19.058494 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257123 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900547315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.1088 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141922 SAMEA13539955 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745434. BACPHLIP temperate score 0.9569113353173286 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539955 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 8.7695900000000009 MAG coverage software Reads (ERR7745434) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_23_1587__NODE_1195_length_39142_cov_5.194112_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585836 sample name Hadza_MoBio_hadza-A-D_B_23_1587__NODE_1195_length_39142_cov_5.194112_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME255258 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp003150355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_virus.1367 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141923 SAMEA13539956 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745434. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539956 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 18.7459 MAG coverage software Reads (ERR7745434) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_B_23_1587__NODE_377_length_87042_cov_11.525407_1 Viral contig found in MAG ERR7745434_bin.84 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585836 sample name Hadza_MoBio_hadza-A-D_B_23_1587__NODE_377_length_87042_cov_11.525407_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.29 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900554205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_provirus.327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141924 SAMEA13539957 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745434. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539957 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 16.6124 MAG coverage software Reads (ERR7745434) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 249 Submitter Id Hadza_MoBio_hadza-A-D_B_23_1587__NODE_74_length_209281_cov_10.203725_1 Viral contig found in MAG ERR7745434_bin.102 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; HMM-based (lower-bound) completeness score 77.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.775 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585836 sample name Hadza_MoBio_hadza-A-D_B_23_1587__NODE_74_length_209281_cov_10.203725_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745434_provirus.74 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141925 SAMEA13539958 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745434. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539958 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 15.565 MAG coverage software Reads (ERR7745434) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-A-D_B_23_1587__NODE_1173_length_39838_cov_9.418953 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585836 sample name Hadza_MoBio_hadza-A-D_B_23_1587__NODE_1173_length_39838_cov_9.418953 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738188_virus.899 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141926 SAMEA13539959 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745434. BACPHLIP temperate score 0.05335306433405912 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539959 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 37.6773 MAG coverage software Reads (ERR7745434) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_B_23_1587__NODE_2071_length_24025_cov_23.109070 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585836 sample name Hadza_MoBio_hadza-A-D_B_23_1587__NODE_2071_length_24025_cov_23.109070 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_provirus.40 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141927 SAMEA13539960 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745434. BACPHLIP temperate score 0.65 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539960 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 109.553 MAG coverage software Reads (ERR7745434) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561092) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_B_23_1587__NODE_558_length_68126_cov_64.557040 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585836 sample name Hadza_MoBio_hadza-A-D_B_23_1587__NODE_558_length_68126_cov_64.557040 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_virus.379 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141928 SAMEA13539961 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745438. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539961 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 11.2994 MAG coverage software Reads (ERR7745438) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560969) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_J_19_1543__NODE_1399_length_36161_cov_6.217243_1 Viral contig found in MAG ERR7745438_bin.202 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585797 sample name Hadza_MoBio_hadza-A-D_J_19_1543__NODE_1399_length_36161_cov_6.217243_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_provirus.2577 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141929 SAMEA13539962 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745438. BACPHLIP temperate score 0.01354854638802992 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539962 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 11.1212 MAG coverage software Reads (ERR7745438) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560969) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_J_19_1543__NODE_210_length_124777_cov_5.820233_1 Viral contig found in MAG ERR7745438_bin.125 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585797 sample name Hadza_MoBio_hadza-A-D_J_19_1543__NODE_210_length_124777_cov_5.820233_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_provirus.210 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141930 SAMEA13539963 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745438. BACPHLIP temperate score 0.01242110588677733 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539963 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 33.5021 MAG coverage software Reads (ERR7745438) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560969) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-A-D_J_19_1543__NODE_584_length_66522_cov_19.582948_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585797 sample name Hadza_MoBio_hadza-A-D_J_19_1543__NODE_584_length_66522_cov_19.582948_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_provirus.512 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141931 SAMEA13539964 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745438. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539964 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 87.6385 MAG coverage software Reads (ERR7745438) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560969) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_J_19_1543__NODE_1111_length_43239_cov_49.464367 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585797 sample name Hadza_MoBio_hadza-A-D_J_19_1543__NODE_1111_length_43239_cov_49.464367 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738222_virus.858 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141932 SAMEA13539965 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745438. BACPHLIP temperate score 0.889977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539965 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 13.1336 MAG coverage software Reads (ERR7745438) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560969) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_J_19_1543__NODE_1350_length_37292_cov_7.717614 Viral contig found in MAG ERR7745438_bin.192 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 82.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585797 sample name Hadza_MoBio_hadza-A-D_J_19_1543__NODE_1350_length_37292_cov_7.717614 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.227 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141933 SAMEA13539966 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745438. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539966 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 8.02255 MAG coverage software Reads (ERR7745438) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560969) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_J_19_1543__NODE_2711_length_21525_cov_4.294107 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585797 sample name Hadza_MoBio_hadza-A-D_J_19_1543__NODE_2711_length_21525_cov_4.294107 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.2674 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141934 SAMEA13539967 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745438. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539967 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 21.6626 MAG coverage software Reads (ERR7745438) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560969) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-A-D_J_19_1543__NODE_700_length_59684_cov_12.484926 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585797 sample name Hadza_MoBio_hadza-A-D_J_19_1543__NODE_700_length_59684_cov_12.484926 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745438_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.487 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141935 SAMEA13539968 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745539. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539968 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 19.1936 MAG coverage software Reads (ERR7745539) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_A_23_1707__NODE_227_length_39100_cov_9.461548_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585950 sample name Hadza_MoBio_hadza-E-H_A_23_1707__NODE_227_length_39100_cov_9.461548_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143483 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium breve vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738155_virus.592 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141936 SAMEA13539969 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745544. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539969 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 9.62961 MAG coverage software Reads (ERR7745544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562240) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 210 Number of CRISPR spacer hits supporting host taxonomy 225 Submitter Id Hadza_MoBio_hadza-A-D_F_12_1633__NODE_1128_length_38061_cov_5.908725_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585877 sample name Hadza_MoBio_hadza-A-D_F_12_1633__NODE_1128_length_38061_cov_5.908725_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp003514385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745544_provirus.1128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141937 SAMEA13539970 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745544. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539970 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 16.9852 MAG coverage software Reads (ERR7745544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562240) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_F_12_1633__NODE_409_length_70289_cov_10.255170_1 Viral contig found in MAG ERR7745544_bin.194 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585877 sample name Hadza_MoBio_hadza-A-D_F_12_1633__NODE_409_length_70289_cov_10.255170_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_provirus.37 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141938 SAMEA13539971 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745544. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539971 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 10.6024 MAG coverage software Reads (ERR7745544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562240) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_F_12_1633__NODE_1267_length_35206_cov_6.187708 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585877 sample name Hadza_MoBio_hadza-A-D_F_12_1633__NODE_1267_length_35206_cov_6.187708 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738208_virus.802 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141939 SAMEA13539972 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7745544. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539972 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 9.39963 MAG coverage software Reads (ERR7745544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562240) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_F_12_1633__NODE_189_length_102080_cov_5.513063 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.972972972972973 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585877 sample name Hadza_MoBio_hadza-A-D_F_12_1633__NODE_189_length_102080_cov_5.513063 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738173_virus.152 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11141940 SAMEA13539973 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745544. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539973 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 100.43 MAG coverage software Reads (ERR7745544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562240) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_F_12_1633__NODE_550_length_59557_cov_61.100353 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.951219512195122 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585877 sample name Hadza_MoBio_hadza-A-D_F_12_1633__NODE_550_length_59557_cov_61.100353 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738208_virus.509 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141941 SAMEA13539974 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745544. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539974 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 17.8275 MAG coverage software Reads (ERR7745544) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562240) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 196 Submitter Id Hadza_MoBio_hadza-A-D_F_12_1633__NODE_989_length_41629_cov_10.696597 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585877 sample name Hadza_MoBio_hadza-A-D_F_12_1633__NODE_989_length_41629_cov_10.696597 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746721_virus.430 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141942 SAMEA13539975 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745545. BACPHLIP temperate score 0.0380538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539975 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 11.6519 MAG coverage software Reads (ERR7745545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559315) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2821 Number of CRISPR spacer hits supporting host taxonomy 587 Submitter Id Hadza_MoBio_hadza-I-L_G_14_2608__NODE_312_length_75945_cov_6.209140_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586318 sample name Hadza_MoBio_hadza-I-L_G_14_2608__NODE_312_length_75945_cov_6.209140_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745545_provirus.312 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141943 SAMEA13539976 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745545. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539976 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 64.4168 MAG coverage software Reads (ERR7745545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559315) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 238 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_G_14_2608__NODE_1133_length_36545_cov_34.652106 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586318 sample name Hadza_MoBio_hadza-I-L_G_14_2608__NODE_1133_length_36545_cov_34.652106 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_provirus.360 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141944 SAMEA13539977 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745545. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539977 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 10.5987 MAG coverage software Reads (ERR7745545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559315) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 338 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-I-L_G_14_2608__NODE_174_length_99330_cov_5.574562 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586318 sample name Hadza_MoBio_hadza-I-L_G_14_2608__NODE_174_length_99330_cov_5.574562 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME111561 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745545_virus.174 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141945 SAMEA13539978 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745545. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539978 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 65.8122 MAG coverage software Reads (ERR7745545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559315) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 136 Submitter Id Hadza_MoBio_hadza-I-L_G_14_2608__NODE_625_length_53852_cov_35.395686 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586318 sample name Hadza_MoBio_hadza-I-L_G_14_2608__NODE_625_length_53852_cov_35.395686 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0345548 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141946 SAMEA13539979 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745545. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539979 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 57.2906 MAG coverage software Reads (ERR7745545) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559315) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_G_14_2608__NODE_935_length_41514_cov_31.386346 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586318 sample name Hadza_MoBio_hadza-I-L_G_14_2608__NODE_935_length_41514_cov_31.386346 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_provirus.169 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141947 SAMEA13539980 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745556. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539980 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 35.1567 MAG coverage software Reads (ERR7745556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_C-REDO_C_9_1537__NODE_421_length_80825_cov_20.472309_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585791 sample name Hadza_MoBio_C-REDO_C_9_1537__NODE_421_length_80825_cov_20.472309_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-877;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745556_provirus.421 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141948 SAMEA13539981 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745556. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539981 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 9.0233 MAG coverage software Reads (ERR7745556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_C-REDO_C_9_1537__NODE_1000_length_46667_cov_4.898583 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585791 sample name Hadza_MoBio_C-REDO_C_9_1537__NODE_1000_length_46667_cov_4.898583 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746739_virus.544 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141949 SAMEA13539982 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745556. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539982 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 33.5731 MAG coverage software Reads (ERR7745556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_C-REDO_C_9_1537__NODE_1645_length_32044_cov_18.974599 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585791 sample name Hadza_MoBio_C-REDO_C_9_1537__NODE_1645_length_32044_cov_18.974599 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747255_bin.83 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-884;s__CAG-884 sp000433875 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_provirus.973 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141950 SAMEA13539983 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745556. BACPHLIP temperate score 0.00991189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539983 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 10.5957 MAG coverage software Reads (ERR7745556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_C-REDO_C_9_1537__NODE_2334_length_23942_cov_5.564132 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585791 sample name Hadza_MoBio_C-REDO_C_9_1537__NODE_2334_length_23942_cov_5.564132 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_provirus.640 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141951 SAMEA13539984 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745556. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539984 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 21.9133 MAG coverage software Reads (ERR7745556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_C-REDO_C_9_1537__NODE_37_length_242777_cov_12.084718 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.7166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585791 sample name Hadza_MoBio_C-REDO_C_9_1537__NODE_37_length_242777_cov_12.084718 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_virus.70 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11141952 SAMEA13539985 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745556. BACPHLIP temperate score 0.15383948336067438 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539985 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 12.1576 MAG coverage software Reads (ERR7745556) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560852) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_C-REDO_C_9_1537__NODE_875_length_51816_cov_6.250565 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585791 sample name Hadza_MoBio_C-REDO_C_9_1537__NODE_875_length_51816_cov_6.250565 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745382_bin.175 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-552;g__UBA10677;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747083_virus.997 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141953 SAMEA13539986 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745559. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539986 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 21.1773 MAG coverage software Reads (ERR7745559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560875) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 139 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Hadza_MoBio_hadza-A-D_L_3_1539__NODE_496_length_60711_cov_13.557872_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585793 sample name Hadza_MoBio_hadza-A-D_L_3_1539__NODE_496_length_60711_cov_13.557872_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0342275 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141954 SAMEA13539987 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745559. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539987 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 8.73814 MAG coverage software Reads (ERR7745559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560875) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_L_3_1539__NODE_877_length_42341_cov_5.037763_1 Viral contig found in MAG ERR7745559_bin.239 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585793 sample name Hadza_MoBio_hadza-A-D_L_3_1539__NODE_877_length_42341_cov_5.037763_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_provirus.766 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141955 SAMEA13539988 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745559. BACPHLIP temperate score 0.09419107100014808 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539988 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 9.98262 MAG coverage software Reads (ERR7745559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560875) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_L_3_1539__NODE_1633_length_27361_cov_5.712615 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585793 sample name Hadza_MoBio_hadza-A-D_L_3_1539__NODE_1633_length_27361_cov_5.712615 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141956 SAMEA13539989 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7745559. BACPHLIP temperate score 0.12878892628021937 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539989 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 9.35867 MAG coverage software Reads (ERR7745559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560875) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-A-D_L_3_1539__NODE_240_length_98686_cov_5.426533 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585793 sample name Hadza_MoBio_hadza-A-D_L_3_1539__NODE_240_length_98686_cov_5.426533 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746012_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11141957 SAMEA13539990 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745559. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539990 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 16.2251 MAG coverage software Reads (ERR7745559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560875) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_L_3_1539__NODE_472_length_62869_cov_9.792601 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585793 sample name Hadza_MoBio_hadza-A-D_L_3_1539__NODE_472_length_62869_cov_9.792601 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141958 SAMEA13539991 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745559. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539991 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:48Z INSDC last update 2022-12-27T01:22:48Z INSDC status public MAG coverage depth 7.86685 MAG coverage software Reads (ERR7745559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560875) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1483 Number of CRISPR spacer hits supporting host taxonomy 98 Submitter Id Hadza_MoBio_hadza-A-D_L_3_1539__NODE_836_length_43799_cov_4.550089 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585793 sample name Hadza_MoBio_hadza-A-D_L_3_1539__NODE_836_length_43799_cov_4.550089 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_virus.836 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141959 SAMEA13539992 1701671 uncultured podovirus This sample represents an uncultured Aeromonas phage phiARM81mr virus assembled from ERR7745559. BACPHLIP temperate score 0.6424559471365638 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539992 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 10.8134 MAG coverage software Reads (ERR7745559) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560875) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 684 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-A-D_L_3_1539__NODE_971_length_39664_cov_6.447723 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585793 sample name Hadza_MoBio_hadza-A-D_L_3_1539__NODE_971_length_39664_cov_6.447723 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME108259 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900313215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_virus.119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Aeromonas phage phiARM81mr virus enrichment approach none ERS11141960 SAMEA13539993 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7745561. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539993 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 441.265 MAG coverage software Reads (ERR7745561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560188) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9493 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_H_4_2261__NODE_38_length_198664_cov_273.770599_1 Viral contig found in MAG ERR7745561_bin.28 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586167 sample name Hadza_MoBio_hadza-E-H_H_4_2261__NODE_38_length_198664_cov_273.770599_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745561_provirus.38 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141961 SAMEA13539994 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745561. BACPHLIP temperate score 0.05947136563876654 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539994 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 125.689 MAG coverage software Reads (ERR7745561) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560188) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_H_4_2261__NODE_377_length_45522_cov_73.412367 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9393939393939394 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586167 sample name Hadza_MoBio_hadza-E-H_H_4_2261__NODE_377_length_45522_cov_73.412367 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745561_virus.377 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141962 SAMEA13539995 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745563. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539995 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 15.6427 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_234_length_100092_cov_9.491446_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_234_length_100092_cov_9.491446_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745989_bin.108 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG806;s__RUG806 sp900313475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745743_provirus.1247 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141963 SAMEA13539996 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745563. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539996 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 74.656 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_64_length_181250_cov_45.649352_1 Viral contig found in MAG ERR7745563_bin.128 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.56 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_64_length_181250_cov_45.649352_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_provirus.117 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141964 SAMEA13539997 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745563. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539997 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 316.503 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_1068_length_41615_cov_187.740503 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_1068_length_41615_cov_187.740503 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.551 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141965 SAMEA13539998 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745563. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539998 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 9.30894 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_1239_length_37384_cov_5.509904 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_1239_length_37384_cov_5.509904 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_virus.1239 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141966 SAMEA13539999 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745563. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13539999 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 38.89 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_1694_length_30667_cov_22.849461 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_1694_length_30667_cov_22.849461 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-451;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745914_virus.1335 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141967 SAMEA13540000 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745563. BACPHLIP temperate score 0.03469162995594714 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540000 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 9.71875 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_2600_length_22205_cov_5.575606 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_2600_length_22205_cov_5.575606 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_provirus.375 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11141968 SAMEA13540001 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745563. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540001 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 66.1462 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_531_length_64458_cov_39.235256 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_531_length_64458_cov_39.235256 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.483 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141969 SAMEA13540002 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745563. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540002 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 64.5341 MAG coverage software Reads (ERR7745563) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561109) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 1028 Submitter Id Hadza_MoBio_hadza-A-D_B_19_1591__NODE_660_length_57376_cov_38.566223 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; HMM-based (lower-bound) completeness score 65.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585840 sample name Hadza_MoBio_hadza-A-D_B_19_1591__NODE_660_length_57376_cov_38.566223 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746465_bin.138 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA3388;s__UBA3388 sp900546465 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.901 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141970 SAMEA13540003 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745565. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540003 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 13.1695 MAG coverage software Reads (ERR7745565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566845) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_C-REDO_G_5_1580__NODE_228_length_80087_cov_7.370966_1 Viral contig found in MAG ERR7745565_bin.49 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585829 sample name Hadza_MoBio_C-REDO_G_5_1580__NODE_228_length_80087_cov_7.370966_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738233_virus.443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141971 SAMEA13540004 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745565. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540004 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 459.499 MAG coverage software Reads (ERR7745565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566845) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 170 Submitter Id Hadza_MoBio_C-REDO_G_5_1580__NODE_89_length_121138_cov_272.297676_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585829 sample name Hadza_MoBio_C-REDO_G_5_1580__NODE_89_length_121138_cov_272.297676_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.1407 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141972 SAMEA13540005 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745565. BACPHLIP temperate score 0.15293544543429416 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540005 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 10.011 MAG coverage software Reads (ERR7745565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566845) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_C-REDO_G_5_1580__NODE_1264_length_29451_cov_5.609348 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585829 sample name Hadza_MoBio_C-REDO_G_5_1580__NODE_1264_length_29451_cov_5.609348 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_provirus.223 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141973 SAMEA13540006 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7745565. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540006 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 160.489 MAG coverage software Reads (ERR7745565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566845) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_G_5_1580__NODE_2125_length_20102_cov_97.538826 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585829 sample name Hadza_MoBio_C-REDO_G_5_1580__NODE_2125_length_20102_cov_97.538826 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745565_virus.2125 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11141974 SAMEA13540007 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745565. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540007 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 18.4636 MAG coverage software Reads (ERR7745565) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566845) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_C-REDO_G_5_1580__NODE_688_length_43084_cov_10.496129 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585829 sample name Hadza_MoBio_C-REDO_G_5_1580__NODE_688_length_43084_cov_10.496129 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145985 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.405 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141975 SAMEA13540008 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745577. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540008 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 89.3595 MAG coverage software Reads (ERR7745577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561808) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-A-D_A_14_1114__NODE_32_length_230795_cov_55.054595_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5172413793103449 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585538 sample name Hadza_MoBio_hadza-A-D_A_14_1114__NODE_32_length_230795_cov_55.054595_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747426_bin.316 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D succinifaciens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_provirus.44 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141976 SAMEA13540009 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745577. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540009 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 17.2472 MAG coverage software Reads (ERR7745577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561808) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_14_1114__NODE_1079_length_39113_cov_10.654191 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585538 sample name Hadza_MoBio_hadza-A-D_A_14_1114__NODE_1079_length_39113_cov_10.654191 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745577_virus.1079 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141977 SAMEA13540010 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 virus assembled from ERR7745577. BACPHLIP temperate score 0.0632649586071869 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540010 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 149.529 MAG coverage software Reads (ERR7745577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561808) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 148 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-A-D_A_14_1114__NODE_1649_length_28792_cov_91.964548 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585538 sample name Hadza_MoBio_hadza-A-D_A_14_1114__NODE_1649_length_28792_cov_91.964548 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_provirus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11141978 SAMEA13540011 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7745577. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540011 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 557.151 MAG coverage software Reads (ERR7745577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561808) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-A-D_A_14_1114__NODE_211_length_111014_cov_339.774854 Viral contig found in MAG ERR7745577_bin.96 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585538 sample name Hadza_MoBio_hadza-A-D_A_14_1114__NODE_211_length_111014_cov_339.774854 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745577_virus.211 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11141979 SAMEA13540012 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745577. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540012 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 44.7663 MAG coverage software Reads (ERR7745577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561808) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_A_14_1114__NODE_342_length_84356_cov_27.237426 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585538 sample name Hadza_MoBio_hadza-A-D_A_14_1114__NODE_342_length_84356_cov_27.237426 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_virus.368 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141980 SAMEA13540013 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745577. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540013 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 16.2235 MAG coverage software Reads (ERR7745577) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561808) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 154 Submitter Id Hadza_MoBio_hadza-A-D_A_14_1114__NODE_594_length_58517_cov_9.879860 Viral contig found in MAG ERR7745577_bin.92 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585538 sample name Hadza_MoBio_hadza-A-D_A_14_1114__NODE_594_length_58517_cov_9.879860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253778 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp003491505 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.741 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141981 SAMEA13540014 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745582. BACPHLIP temperate score 0.03986784140969163 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540014 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 33.1962 MAG coverage software Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 186 Number of CRISPR spacer hits supporting host taxonomy 251 Submitter Id Hadza_MoBio_hadza-A-D_F_6_1630__NODE_1_length_883224_cov_22.191299_1 Viral contig found in MAG ERR7745582_bin.216 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585874 sample name Hadza_MoBio_hadza-A-D_F_6_1630__NODE_1_length_883224_cov_22.191299_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0318998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141982 SAMEA13540015 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745582. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540015 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 43.1825 MAG coverage software Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 183 Number of CRISPR spacer hits supporting host taxonomy 962 Submitter Id Hadza_MoBio_hadza-A-D_F_6_1630__NODE_299_length_75765_cov_28.399522_1 Viral contig found in MAG ERR7745582_bin.217 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585874 sample name Hadza_MoBio_hadza-A-D_F_6_1630__NODE_299_length_75765_cov_28.399522_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0345129 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141983 SAMEA13540016 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745582. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540016 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 18.5087 MAG coverage software Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_F_6_1630__NODE_781_length_47388_cov_12.122382_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585874 sample name Hadza_MoBio_hadza-A-D_F_6_1630__NODE_781_length_47388_cov_12.122382_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745582_provirus.781 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141984 SAMEA13540017 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745582. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540017 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 10.8801 MAG coverage software Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_F_6_1630__NODE_126_length_112161_cov_7.041406 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585874 sample name Hadza_MoBio_hadza-A-D_F_6_1630__NODE_126_length_112161_cov_7.041406 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738210_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141985 SAMEA13540018 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745582. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540018 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 59.1302 MAG coverage software Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-A-D_F_6_1630__NODE_1727_length_30044_cov_39.883105 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585874 sample name Hadza_MoBio_hadza-A-D_F_6_1630__NODE_1727_length_30044_cov_39.883105 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745582_virus.1727 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141986 SAMEA13540019 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745582. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540019 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 12.6962 MAG coverage software Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-A-D_F_6_1630__NODE_2092_length_26455_cov_8.358139 Viral contig found in MAG ERR7745582_bin.97 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585874 sample name Hadza_MoBio_hadza-A-D_F_6_1630__NODE_2092_length_26455_cov_8.358139 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745556_provirus.421 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141987 SAMEA13540020 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7745582. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540020 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 10.6257 MAG coverage software Reads (ERR7745582) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561354) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 73 Number of CRISPR spacer hits supporting host taxonomy 150 Submitter Id Hadza_MoBio_hadza-A-D_F_6_1630__NODE_484_length_60588_cov_6.955149 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585874 sample name Hadza_MoBio_hadza-A-D_F_6_1630__NODE_484_length_60588_cov_6.955149 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11141988 SAMEA13540021 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745588. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540021 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 20.0915 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 112 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_1108_length_48814_cov_11.445473_1 Viral contig found in MAG ERR7745588_bin.43 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_1108_length_48814_cov_11.445473_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_provirus.1015 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141989 SAMEA13540022 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745588. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540022 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 87.6309 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_41_length_241891_cov_50.762015_1 Viral contig found in MAG ERR7745588_bin.60 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_41_length_241891_cov_50.762015_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_provirus.41 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141990 SAMEA13540023 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745588. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540023 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 31.4484 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 584 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_926_length_55036_cov_18.528685_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5217391304347826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_926_length_55036_cov_18.528685_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141991 SAMEA13540024 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745588. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540024 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 10.5266 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_1236_length_45752_cov_5.902157 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_1236_length_45752_cov_5.902157 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.1351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141992 SAMEA13540025 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745588. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540025 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 135.76 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 286 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_1724_length_36298_cov_103.276773 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_1724_length_36298_cov_103.276773 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.943 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11141993 SAMEA13540026 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745588. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540026 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 347.44 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_2254_length_29487_cov_197.887283 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 82.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4705882352941176 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_2254_length_29487_cov_197.887283 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.1155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141994 SAMEA13540027 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745588. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540027 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 110.463 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_307_length_100560_cov_62.610919 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.9240506329113924 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_307_length_100560_cov_62.610919 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.457 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11141995 SAMEA13540028 2133760 Siphoviridae environmental samples This sample represents an uncultured Clostridium phage phiCp-B virus assembled from ERR7745588. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540028 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 11.4805 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_4069_length_17885_cov_6.454290 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_4069_length_17885_cov_6.454290 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745648_bin.119 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_virus.4069 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Clostridium phage phiCp-B virus enrichment approach none ERS11141996 SAMEA13540029 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745588. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540029 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 14.4033 MAG coverage software Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_4_1104__NODE_78_length_189654_cov_8.213982 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585528 sample name Hadza_MoBio_hadza-A-D_A_4_1104__NODE_78_length_189654_cov_8.213982 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.166 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141997 SAMEA13540030 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745594. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540030 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 11.9592 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_1193_length_47478_cov_6.993186_1 Viral contig found in MAG ERR7745594_bin.117 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9583333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_1193_length_47478_cov_6.993186_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.2541 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141998 SAMEA13540031 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745594. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540031 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 26.5479 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_201_length_155673_cov_15.505154_1 Viral contig found in MAG ERR7745594_bin.88 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_201_length_155673_cov_15.505154_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_provirus.201 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11141999 SAMEA13540032 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745594. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540032 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 12.4836 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 405 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_44_length_302629_cov_15.297043_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_44_length_302629_cov_15.297043_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_provirus.23 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142000 SAMEA13540033 2100421 uncultured Caudovirales phage This sample represents an uncultured Studiervirinae provirus assembled from ERR7745594. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540033 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 35.8906 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_92_length_213044_cov_20.901642_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_92_length_213044_cov_20.901642_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147598 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_provirus.92 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae; Studiervirinae virus enrichment approach none ERS11142001 SAMEA13540034 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745594. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540034 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 31.8741 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_1462_length_40886_cov_18.679262 Viral contig found in MAG ERR7745594_bin.40 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_1462_length_40886_cov_18.679262 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME192801 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp000432135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_virus.1462 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142002 SAMEA13540035 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745594. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540035 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 179.069 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 313 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_1940_length_33254_cov_106.530639 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_1940_length_33254_cov_106.530639 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME067489 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-217;s__CAG-217 sp000436335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_virus.1940 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142003 SAMEA13540036 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745594. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540036 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 49.4039 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_347_length_112201_cov_28.892672 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_347_length_112201_cov_28.892672 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738210_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142004 SAMEA13540037 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745594. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540037 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 11.2806 MAG coverage software Reads (ERR7745594) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560506) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_E_24_1866__NODE_637_length_75343_cov_6.559350 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586042 sample name Hadza_MoBio_hadza-E-H_E_24_1866__NODE_637_length_75343_cov_6.559350 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_virus.637 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142005 SAMEA13540038 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745596. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540038 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 25.5019 MAG coverage software Reads (ERR7745596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567174) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_181_length_113394_cov_14.987266_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.32432432432432434 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787349 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_181_length_113394_cov_14.987266_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0377001 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142006 SAMEA13540039 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona provirus assembled from ERR7745596. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540039 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 24.6619 MAG coverage software Reads (ERR7745596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567174) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 179 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_541_length_53030_cov_14.828565_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787349 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_541_length_53030_cov_14.828565_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001575 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;s__Mediterraneibacter faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745596_provirus.541 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11142007 SAMEA13540040 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745596. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540040 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 101.011 MAG coverage software Reads (ERR7745596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567174) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 812 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_178_length_113673_cov_60.026709 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787349 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_178_length_113673_cov_60.026709 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0378844 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142008 SAMEA13540041 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745596. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540041 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 427.411 MAG coverage software Reads (ERR7745596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567174) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_53_length_188618_cov_251.669987 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 27 number of unique standard tRNAs extracted 20 percent of BLAST hits supporting viral taxonomy 0.4927536231884058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787349 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_53_length_188618_cov_251.669987 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola dorei vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0379517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142009 SAMEA13540042 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745596. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540042 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 455.045 MAG coverage software Reads (ERR7745596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567174) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 898 Number of CRISPR spacer hits supporting host taxonomy 129 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_753_length_41006_cov_268.501234 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787349 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_15_CHE1020TZ__NODE_753_length_41006_cov_268.501234 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0345445 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142010 SAMEA13540043 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745603. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540043 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 12.7176 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_112_length_130869_cov_7.382630_1 Viral contig found in MAG ERR7745603_bin.69 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_112_length_130869_cov_7.382630_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_provirus.37 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142011 SAMEA13540044 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745603. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540044 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 14.1884 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_398_length_72464_cov_7.980204_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_398_length_72464_cov_7.980204_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024527 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552675 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.1298 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142012 SAMEA13540045 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540045 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 27.1942 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_9_length_308769_cov_15.258397_1 Viral contig found in MAG ERR7745603_bin.113 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_9_length_308769_cov_15.258397_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME039567 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632;s__CAG-632 sp900539185 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745603_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142013 SAMEA13540046 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745603. BACPHLIP temperate score 0.00247797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540046 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 11.1872 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_1233_length_34946_cov_6.311394 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_1233_length_34946_cov_6.311394 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.985 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142014 SAMEA13540047 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745603. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540047 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 9.1090699999999991 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_1622_length_29003_cov_5.074915 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_1622_length_29003_cov_5.074915 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745603_virus.1622 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142015 SAMEA13540048 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7745603. BACPHLIP temperate score 0.6743672824538927 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540048 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 58.554 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 393 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_2291_length_22436_cov_37.452569 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_2291_length_22436_cov_37.452569 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.929 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142016 SAMEA13540049 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540049 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 17.2053 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_379_length_73941_cov_9.782925 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_379_length_73941_cov_9.782925 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745603_virus.379 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142017 SAMEA13540050 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745603. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540050 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 91.8931 MAG coverage software Reads (ERR7745603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560391) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 88 Submitter Id Hadza_MoBio_hadza-E-H_A_4_1815__NODE_811_length_46191_cov_52.734115 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586015 sample name Hadza_MoBio_hadza-E-H_A_4_1815__NODE_811_length_46191_cov_52.734115 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.832 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142018 SAMEA13540051 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745613. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540051 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 57.2699 MAG coverage software Reads (ERR7745613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 145 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_A_6_1816__NODE_162_length_145656_cov_32.545930_1 Viral contig found in MAG ERR7745613_bin.117 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5247524752475248 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586016 sample name Hadza_MoBio_hadza-E-H_A_6_1816__NODE_162_length_145656_cov_32.545930_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142482 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus paragasseri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738237_provirus.155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142019 SAMEA13540052 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745613. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540052 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 110.319 MAG coverage software Reads (ERR7745613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 319 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_A_6_1816__NODE_59_length_237141_cov_62.914175_1 Viral contig found in MAG ERR7745613_bin.104 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586016 sample name Hadza_MoBio_hadza-E-H_A_6_1816__NODE_59_length_237141_cov_62.914175_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745975_bin.137 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;s__CAG-488 sp000434055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745613_provirus.59 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142020 SAMEA13540053 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745613. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540053 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 19.3405 MAG coverage software Reads (ERR7745613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_A_6_1816__NODE_1320_length_36818_cov_10.975940 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586016 sample name Hadza_MoBio_hadza-E-H_A_6_1816__NODE_1320_length_36818_cov_10.975940 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900542795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746779_virus.1100 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142021 SAMEA13540054 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745613. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540054 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 7.31881 MAG coverage software Reads (ERR7745613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 87 Submitter Id Hadza_MoBio_hadza-E-H_A_6_1816__NODE_2549_length_21752_cov_4.069066 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586016 sample name Hadza_MoBio_hadza-E-H_A_6_1816__NODE_2549_length_21752_cov_4.069066 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159485 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.546 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142022 SAMEA13540055 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745613. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540055 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 53.6227 MAG coverage software Reads (ERR7745613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 454 Submitter Id Hadza_MoBio_hadza-E-H_A_6_1816__NODE_414_length_84923_cov_37.069385 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-26 completeness approach CheckV; HMM-based (lower-bound) completeness score 54.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.4375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586016 sample name Hadza_MoBio_hadza-E-H_A_6_1816__NODE_414_length_84923_cov_37.069385 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745613_virus.414 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142023 SAMEA13540056 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745613. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540056 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 41.0977 MAG coverage software Reads (ERR7745613) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_A_6_1816__NODE_699_length_61038_cov_33.913929 Viral contig found in MAG ERR7745613_bin.96 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586016 sample name Hadza_MoBio_hadza-E-H_A_6_1816__NODE_699_length_61038_cov_33.913929 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745989_bin.40 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS2068;s__UMGS2068 sp900769635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745613_virus.699 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142024 SAMEA13540057 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745614. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540057 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 25.1612 MAG coverage software Reads (ERR7745614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562173) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_L_1_1540__NODE_29_length_306229_cov_14.880723_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9318181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585794 sample name Hadza_MoBio_hadza-A-D_L_1_1540__NODE_29_length_306229_cov_14.880723_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME256593 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp900547385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_provirus.6 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142025 SAMEA13540058 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745614. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540058 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 25.9217 MAG coverage software Reads (ERR7745614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562173) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-A-D_L_1_1540__NODE_563_length_57799_cov_15.544836_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585794 sample name Hadza_MoBio_hadza-A-D_L_1_1540__NODE_563_length_57799_cov_15.544836_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745614_provirus.563 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142026 SAMEA13540059 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745614. BACPHLIP temperate score 0.3125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540059 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 26.764 MAG coverage software Reads (ERR7745614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562173) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-A-D_L_1_1540__NODE_1223_length_34059_cov_15.701695 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4117647058823529 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585794 sample name Hadza_MoBio_hadza-A-D_L_1_1540__NODE_1223_length_34059_cov_15.701695 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746233_virus.358 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142027 SAMEA13540060 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745614. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540060 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 9.63764 MAG coverage software Reads (ERR7745614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562173) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_L_1_1540__NODE_2047_length_23522_cov_5.523694 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585794 sample name Hadza_MoBio_hadza-A-D_L_1_1540__NODE_2047_length_23522_cov_5.523694 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738200_provirus.73 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142028 SAMEA13540061 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745614. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540061 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 10.1936 MAG coverage software Reads (ERR7745614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562173) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_L_1_1540__NODE_309_length_83800_cov_5.986001 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585794 sample name Hadza_MoBio_hadza-A-D_L_1_1540__NODE_309_length_83800_cov_5.986001 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738613_virus.238 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142029 SAMEA13540062 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745614. BACPHLIP temperate score 0.14430120315873837 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540062 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 15.7575 MAG coverage software Reads (ERR7745614) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562173) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_L_1_1540__NODE_61_length_198989_cov_9.009215 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 28 number of unique standard tRNAs extracted 20 percent of BLAST hits supporting viral taxonomy 0.4791666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585794 sample name Hadza_MoBio_hadza-A-D_L_1_1540__NODE_61_length_198989_cov_9.009215 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000448 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900066885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.45 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142030 SAMEA13540063 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745621. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540063 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 62.2476 MAG coverage software Reads (ERR7745621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561324) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_MoBio_hadza-I-L_J_14_1278__NODE_105_length_102584_cov_37.486416_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585695 sample name Hadza_MoBio_hadza-I-L_J_14_1278__NODE_105_length_102584_cov_37.486416_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738236_provirus.42 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142031 SAMEA13540064 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745621. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540064 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 53.7284 MAG coverage software Reads (ERR7745621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561324) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_J_14_1278__NODE_248_length_49053_cov_31.569218 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585695 sample name Hadza_MoBio_hadza-I-L_J_14_1278__NODE_248_length_49053_cov_31.569218 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745621_virus.248 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142032 SAMEA13540065 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745621. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540065 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 14.4203 MAG coverage software Reads (ERR7745621) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561324) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-I-L_J_14_1278__NODE_695_length_19318_cov_11.762746 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585695 sample name Hadza_MoBio_hadza-I-L_J_14_1278__NODE_695_length_19318_cov_11.762746 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745561_bin.8 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746794_virus.495 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142033 SAMEA13540066 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745625. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540066 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 22.5146 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_38_length_211868_cov_13.177316_1 Viral contig found in MAG ERR7745625_bin.113 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.627906976744186 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_38_length_211868_cov_13.177316_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.1202 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142034 SAMEA13540067 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745625. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540067 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 12.0715 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_678_length_59003_cov_6.897787_1 Viral contig found in MAG ERR7745625_bin.144 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_678_length_59003_cov_6.897787_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738529_provirus.276 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142035 SAMEA13540068 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745625. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540068 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 53.4192 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 91 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_1154_length_43085_cov_30.962333 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_1154_length_43085_cov_30.962333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142036 SAMEA13540069 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745625. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540069 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 19.2563 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_165_length_118184_cov_11.037932 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 13 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.6949152542372882 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_165_length_118184_cov_11.037932 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0379068 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142037 SAMEA13540070 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745625. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540070 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 42.7368 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_199_length_109776_cov_24.320960 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_199_length_109776_cov_24.320960 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738240_virus.91 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142038 SAMEA13540071 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745625. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540071 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:47Z INSDC last update 2022-12-27T01:22:47Z INSDC status public MAG coverage depth 24.0729 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_2758_length_23665_cov_14.343225 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_2758_length_23665_cov_14.343225 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745625_virus.2758 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142039 SAMEA13540072 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745625. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540072 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 18.7856 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 1132 Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_378_length_81425_cov_21.584808 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_378_length_81425_cov_21.584808 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142040 SAMEA13540073 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7745625. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540073 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 174.496 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_5265_length_14533_cov_99.662839 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_5265_length_14533_cov_99.662839 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_virus.6384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11142041 SAMEA13540074 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745625. BACPHLIP temperate score 0.05708838203908831 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540074 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 15.8101 MAG coverage software Reads (ERR7745625) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566938) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_C-REDO_D_2_1542__NODE_677_length_59028_cov_9.019677 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585796 sample name Hadza_MoBio_C-REDO_D_2_1542__NODE_677_length_59028_cov_9.019677 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142042 SAMEA13540075 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745634. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540075 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 20.021 MAG coverage software Reads (ERR7745634) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560393) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_C_8_1833__NODE_99_length_77468_cov_11.449716_1 Viral contig found in MAG ERR7745634_bin.14 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586029 sample name Hadza_MoBio_hadza-E-H_C_8_1833__NODE_99_length_77468_cov_11.449716_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745561_provirus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142043 SAMEA13540076 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745648. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540076 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 68.5584 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_121_length_188042_cov_41.463288_1 Viral contig found in MAG ERR7745648_bin.202 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_121_length_188042_cov_41.463288_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747615_bin.162 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS363;s__UMGS363 sp900768245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_provirus.121 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142044 SAMEA13540077 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745648. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540077 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 58.8172 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_218_length_142038_cov_35.489740_1_1 Viral contig found in MAG ERR7745648_bin.202 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_218_length_142038_cov_35.489740_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747615_bin.162 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS363;s__UMGS363 sp900768245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_provirus.218 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142045 SAMEA13540078 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745648. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540078 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 26.354 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_410_length_98560_cov_15.148696_1 Viral contig found in MAG ERR7745648_bin.223 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_410_length_98560_cov_15.148696_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745888_bin.58 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B;s__Enterococcus_B hirae vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745621_provirus.14 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142046 SAMEA13540079 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745648. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540079 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 10.9842 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_941_length_61990_cov_6.389773_1 Viral contig found in MAG ERR7745648_bin.228 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 50.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_941_length_61990_cov_6.389773_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091217 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973;s__UMGS973 sp900547295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738591_provirus.382 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142047 SAMEA13540080 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745648. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540080 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 186.191 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1088_length_56025_cov_106.054837 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; ITR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9534883720930232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1088_length_56025_cov_106.054837 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745438_bin.61 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp004553545 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745556_virus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142048 SAMEA13540081 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745648. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540081 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 33.8221 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 281 Number of CRISPR spacer hits supporting host taxonomy 142 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1491_length_46029_cov_20.048377 Viral contig found in MAG ERR7745648_bin.229 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1491_length_46029_cov_20.048377 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.1491 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142049 SAMEA13540082 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745648. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540082 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 9.92195 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1814_length_40188_cov_5.733739 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1814_length_40188_cov_5.733739 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142050 SAMEA13540083 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745648. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540083 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 18.4893 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 221 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1988_length_37221_cov_10.645972 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_1988_length_37221_cov_10.645972 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142051 SAMEA13540084 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7745648. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540084 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 26.2271 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_25620_length_3430_cov_16.072771 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_25620_length_3430_cov_16.072771 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_virus.22944 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11142052 SAMEA13540085 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745648. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540085 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 5.81283 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_3836_length_20875_cov_3.130253 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_3836_length_20875_cov_3.130253 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.945 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142053 SAMEA13540086 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745648. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540086 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 63.0466 MAG coverage software Reads (ERR7745648) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561548) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Hadza_MoBio_hadza-I-L_B_22_1164__NODE_836_length_67507_cov_36.866751 Viral contig found in MAG ERR7745648_bin.190 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48148148148148145 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585588 sample name Hadza_MoBio_hadza-I-L_B_22_1164__NODE_836_length_67507_cov_36.866751 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.836 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142054 SAMEA13540087 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7745675. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540087 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 13.0831 MAG coverage software Reads (ERR7745675) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560209) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_F_24_2253__NODE_161_length_123616_cov_7.573204_2 Viral contig found in MAG ERR7745675_bin.15 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8305084745762712 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586165 sample name Hadza_MoBio_hadza-E-H_F_24_2253__NODE_161_length_123616_cov_7.573204_2 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745922_virus.576 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11142055 SAMEA13540088 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745675. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540088 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 100.965 MAG coverage software Reads (ERR7745675) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560209) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 142 Submitter Id Hadza_MoBio_hadza-E-H_F_24_2253__NODE_337_length_88919_cov_67.932937_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586165 sample name Hadza_MoBio_hadza-E-H_F_24_2253__NODE_337_length_88919_cov_67.932937_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745384_provirus.313 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142056 SAMEA13540089 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745675. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540089 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 592.245 MAG coverage software Reads (ERR7745675) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560209) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_MoBio_hadza-E-H_F_24_2253__NODE_676_length_60650_cov_375.683836_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586165 sample name Hadza_MoBio_hadza-E-H_F_24_2253__NODE_676_length_60650_cov_375.683836_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142057 SAMEA13540090 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745675. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540090 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 11.4993 MAG coverage software Reads (ERR7745675) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560209) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 172 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-E-H_F_24_2253__NODE_1219_length_42303_cov_6.608369 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 81.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586165 sample name Hadza_MoBio_hadza-E-H_F_24_2253__NODE_1219_length_42303_cov_6.608369 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142058 SAMEA13540091 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745675. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540091 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 29.3528 MAG coverage software Reads (ERR7745675) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560209) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-E-H_F_24_2253__NODE_2103_length_27933_cov_17.980076 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586165 sample name Hadza_MoBio_hadza-E-H_F_24_2253__NODE_2103_length_27933_cov_17.980076 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0307965 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142059 SAMEA13540092 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745675. BACPHLIP temperate score 0.07943336174904672 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540092 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 26.7321 MAG coverage software Reads (ERR7745675) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560209) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_MoBio_hadza-E-H_F_24_2253__NODE_3057_length_20254_cov_15.920900 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586165 sample name Hadza_MoBio_hadza-E-H_F_24_2253__NODE_3057_length_20254_cov_15.920900 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745675_virus.3057 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142060 SAMEA13540093 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745675. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540093 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 23.1653 MAG coverage software Reads (ERR7745675) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560209) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 79 Submitter Id Hadza_MoBio_hadza-E-H_F_24_2253__NODE_586_length_65076_cov_13.614656 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586165 sample name Hadza_MoBio_hadza-E-H_F_24_2253__NODE_586_length_65076_cov_13.614656 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745675_virus.586 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142061 SAMEA13540094 336724 Myoviridae environmental samples This sample represents an uncultured Bacillus virus G provirus assembled from ERR7745687. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540094 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 144.239 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_116_length_191092_cov_85.171405_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 96.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7358490566037735 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_116_length_191092_cov_85.171405_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_provirus.116 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Donellivirus; Bacillus virus G virus enrichment approach none ERS11142062 SAMEA13540095 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745687. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540095 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 385.834 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 111 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_454_length_90324_cov_249.305240_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_454_length_90324_cov_249.305240_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142063 SAMEA13540096 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745687. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540096 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 24.698 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 62 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_82_length_219483_cov_14.695122_1_1 Viral contig found in MAG ERR7745687_bin.294 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_82_length_219483_cov_14.695122_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738192_bin.62 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732;s__UBA9732 sp001940825 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738213_provirus.55 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142064 SAMEA13540097 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.8636976579134139 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540097 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 20.6878 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 145 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1203_length_47662_cov_12.083451 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5227272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1203_length_47662_cov_12.083451 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-4429795 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142065 SAMEA13540098 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.1088591976631789 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540098 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 291.238 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1322_length_44450_cov_175.929281 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.34782608695652173 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1322_length_44450_cov_175.929281 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1322 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142066 SAMEA13540099 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745687. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540099 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 109.422 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_145_length_167155_cov_64.392673 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.6865671641791045 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_145_length_167155_cov_64.392673 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.145 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142067 SAMEA13540100 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540100 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 12.4827 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1594_length_38443_cov_7.330736 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1594_length_38443_cov_7.330736 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1594 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142068 SAMEA13540101 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540101 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 15.8425 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1419 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1716_length_36066_cov_9.684820 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1716_length_36066_cov_9.684820 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.493 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142069 SAMEA13540102 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.1370737509399937 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540102 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 12.7049 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 241 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1908_length_33293_cov_7.425518 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_1908_length_33293_cov_7.425518 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142070 SAMEA13540103 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7745687. BACPHLIP temperate score 0.12698150709611442 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540103 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 10.0921 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_2487_length_27165_cov_5.956807 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_2487_length_27165_cov_5.956807 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_provirus.1304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142071 SAMEA13540104 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745687. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540104 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 19.0427 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_304_length_113885_cov_11.254762 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9777777777777776 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_304_length_113885_cov_11.254762 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142072 SAMEA13540105 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540105 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 7.22464 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_3502_length_20961_cov_4.075800 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_3502_length_20961_cov_4.075800 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.3609 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142073 SAMEA13540106 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540106 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 132.939 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_452_length_90472_cov_83.033774 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6071428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_452_length_90472_cov_83.033774 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745990_bin.104 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1731;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.452 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142074 SAMEA13540107 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540107 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 74.6296 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_66_length_233716_cov_44.105291 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.492063492063492 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_66_length_233716_cov_44.105291 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000109 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;s__Catenibacterium mitsuokai vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_virus.36 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142075 SAMEA13540108 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745687. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540108 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 23.9694 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_79_length_220340_cov_14.658413 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_79_length_220340_cov_14.658413 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142076 SAMEA13540109 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745687. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540109 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 15.1161 MAG coverage software Reads (ERR7745687) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561781) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 104 Submitter Id Hadza_MoBio_hadza-A-D_G_6_1094__NODE_974_length_55466_cov_8.916608 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585518 sample name Hadza_MoBio_hadza-A-D_G_6_1094__NODE_974_length_55466_cov_8.916608 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME013942 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724;s__CAG-724 sp003524145 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.477 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142077 SAMEA13540110 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745719. BACPHLIP temperate score 0.16243983917627094 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540110 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 21.0958 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1398_length_47045_cov_12.622147_1 Viral contig found in MAG ERR7745719_bin.173 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1398_length_47045_cov_12.622147_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747426_bin.275 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2883;s__UBA2883 sp900768915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.108 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142078 SAMEA13540111 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7745719. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540111 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 27.6658 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 119 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_331_length_109901_cov_16.545536_1 Viral contig found in MAG ERR7745719_bin.190 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_331_length_109901_cov_16.545536_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.1266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11142079 SAMEA13540112 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745719. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540112 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 12.5511 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 205 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1059_length_57493_cov_7.485980 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5128205128205128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1059_length_57493_cov_7.485980 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.1178 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142080 SAMEA13540113 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745719. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540113 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 119.953 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 315 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1560_length_43408_cov_70.990746 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1560_length_43408_cov_70.990746 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.928 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142081 SAMEA13540114 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745719. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540114 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 38.7895 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1731_length_40124_cov_23.619447 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_1731_length_40124_cov_23.619447 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.2031 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142082 SAMEA13540115 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745719. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540115 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 96.531 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_2113_length_34575_cov_56.350687 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_2113_length_34575_cov_56.350687 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME079077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000434935 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.2011 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142083 SAMEA13540116 2133760 Siphoviridae environmental samples This sample represents an uncultured Erysipelothrix phage SE-1 virus assembled from ERR7745719. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540116 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 8.22699 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_3143_length_25415_cov_4.670771 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_3143_length_25415_cov_4.670771 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-605;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_virus.1576 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Erysipelothrix phage SE-1 virus enrichment approach none ERS11142084 SAMEA13540117 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745719. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540117 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 12.801 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_4006_length_20587_cov_7.744320 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_4006_length_20587_cov_7.744320 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.4006 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142086 SAMEA13540119 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745722. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540119 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 11.5632 MAG coverage software Reads (ERR7745722) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559305) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_I_2_2614__NODE_122_length_78540_cov_5.818042_1 Viral contig found in MAG ERR7745722_bin.26 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586324 sample name Hadza_MoBio_hadza-I-L_I_2_2614__NODE_122_length_78540_cov_5.818042_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME177178 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A;s__Enterococcus_A avium vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745722_provirus.122 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142087 SAMEA13540120 2133760 Siphoviridae environmental samples This sample represents an uncultured Lactobacillus phage LR1 provirus assembled from ERR7745722. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540120 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 26.6327 MAG coverage software Reads (ERR7745722) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559305) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_I_2_2614__NODE_70_length_122982_cov_13.518075_1 Viral contig found in MAG ERR7745722_bin.11 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586324 sample name Hadza_MoBio_hadza-I-L_I_2_2614__NODE_70_length_122982_cov_13.518075_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745722_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745722_provirus.70 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lactobacillus phage LR1 virus enrichment approach none ERS11142088 SAMEA13540121 336724 Myoviridae environmental samples This sample represents an uncultured Lactobacillus phage vB_Lcr_AB1 virus assembled from ERR7745722. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540121 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 10.4469 MAG coverage software Reads (ERR7745722) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559305) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_I_2_2614__NODE_233_length_45587_cov_5.238189 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 62.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586324 sample name Hadza_MoBio_hadza-I-L_I_2_2614__NODE_233_length_45587_cov_5.238189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745722_virus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lactobacillus phage vB_Lcr_AB1 virus enrichment approach none ERS11142089 SAMEA13540122 1701671 uncultured podovirus This sample represents an uncultured Uetakevirus virus assembled from ERR7745722. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540122 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 49.8321 MAG coverage software Reads (ERR7745722) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559305) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2255 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_I_2_2614__NODE_279_length_39344_cov_22.561642 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586324 sample name Hadza_MoBio_hadza-I-L_I_2_2614__NODE_279_length_39344_cov_22.561642 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745722_virus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Uetakevirus virus enrichment approach none ERS11142090 SAMEA13540123 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745743. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540123 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 18.7126 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_102_length_175734_cov_10.993926_1 Viral contig found in MAG ERR7745743_bin.216 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_102_length_175734_cov_10.993926_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_virus.2186 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142091 SAMEA13540124 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745743. BACPHLIP temperate score 0.12951046580442682 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540124 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 23.2956 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_237_length_117625_cov_13.478928_1 Viral contig found in MAG ERR7745743_bin.20 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_237_length_117625_cov_13.478928_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746433_provirus.452 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142092 SAMEA13540125 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis provirus assembled from ERR7745743. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540125 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 19.8405 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 88 Number of CRISPR spacer hits supporting host taxonomy 338 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_489_length_78521_cov_11.927936_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8431372549019608 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_489_length_78521_cov_11.927936_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745881_provirus.375 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11142093 SAMEA13540126 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7745743. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540126 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 27.7449 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 467 Number of CRISPR spacer hits supporting host taxonomy 1342 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_1204_length_47219_cov_16.367273 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5490196078431373 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_1204_length_47219_cov_16.367273 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11142094 SAMEA13540127 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745743. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540127 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 247.603 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_1462_length_41615_cov_144.200082 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_1462_length_41615_cov_144.200082 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.551 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142095 SAMEA13540128 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745743. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540128 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 14.9416 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_1753_length_36847_cov_8.753413 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_1753_length_36847_cov_8.753413 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.1416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142096 SAMEA13540129 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745743. BACPHLIP temperate score 0.05495594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540129 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 21.2821 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_2117_length_32900_cov_12.491728 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_2117_length_32900_cov_12.491728 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.1219 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142097 SAMEA13540130 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745743. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540130 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 24.5597 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_2836_length_26963_cov_14.796139 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_2836_length_26963_cov_14.796139 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142098 SAMEA13540131 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745743. BACPHLIP temperate score 0.6 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540131 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 11.6805 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_393_length_89545_cov_6.728082 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8985507246376812 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_393_length_89545_cov_6.728082 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270963 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;s__Lachnospira sp900545725 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738181_provirus.138 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142099 SAMEA13540132 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745743. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540132 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 31.2551 MAG coverage software Reads (ERR7745743) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-A-D_B_15_1593__NODE_836_length_58529_cov_18.206374 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48484848484848486 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585842 sample name Hadza_MoBio_hadza-A-D_B_15_1593__NODE_836_length_58529_cov_18.206374 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142100 SAMEA13540133 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745755. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540133 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 106.609 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_123_length_194594_cov_65.446228_1 Viral contig found in MAG ERR7745755_bin.125 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8809523809523809 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_123_length_194594_cov_65.446228_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745755_provirus.123 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142101 SAMEA13540134 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7745755. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540134 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 11.0129 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_272_length_132929_cov_6.369012_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8923076923076924 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_272_length_132929_cov_6.369012_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME166984 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_I vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745755_provirus.272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11142102 SAMEA13540135 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745755. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540135 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 19.7656 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 350 Number of CRISPR spacer hits supporting host taxonomy 578 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_77_length_234124_cov_11.743573_1 Viral contig found in MAG ERR7745755_bin.198 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_77_length_234124_cov_11.743573_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME111561 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745755_provirus.77 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142103 SAMEA13540136 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7745755. BACPHLIP temperate score 0.01993392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540136 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 8.626 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_1051_length_59634_cov_4.849690 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_1051_length_59634_cov_4.849690 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373831 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11142104 SAMEA13540137 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745755. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540137 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 25.2792 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 155 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_1543_length_44499_cov_15.772815 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_1543_length_44499_cov_15.772815 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738352_provirus.448 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142105 SAMEA13540138 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745755. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540138 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 14.8034 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_178_length_163373_cov_8.819530 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 13 number of unique standard tRNAs extracted 11 percent of BLAST hits supporting viral taxonomy 0.7017543859649122 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_178_length_163373_cov_8.819530 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745755_virus.178 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142106 SAMEA13540139 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745755. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540139 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 22.8307 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_2085_length_35496_cov_14.038059 Viral contig found in MAG ERR7745755_bin.102 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 93.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_2085_length_35496_cov_14.038059 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738167_provirus.974 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142107 SAMEA13540140 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745755. BACPHLIP temperate score 0.038218149912259 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540140 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 13.7762 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 319 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_2666_length_28755_cov_8.605028 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5217391304347826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_2666_length_28755_cov_8.605028 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.2963 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142108 SAMEA13540141 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745755. BACPHLIP temperate score 0.1247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540141 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 7.89875 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 125 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_3632_length_21869_cov_4.457048 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_3632_length_21869_cov_4.457048 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_virus.1544 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142109 SAMEA13540142 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745755. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540142 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 6247.95 MAG coverage software Reads (ERR7745755) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567306) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_549_length_87891_cov_3598.597695 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8536585365853658 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787380 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_23_RAJ1014YZ__NODE_549_length_87891_cov_3598.597695 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745755_virus.549 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142110 SAMEA13540143 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745759. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540143 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 341.722 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 329 Number of CRISPR spacer hits supporting host taxonomy 175 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_172_length_153099_cov_220.004757_1 Viral contig found in MAG ERR7745759_bin.35 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_172_length_153099_cov_220.004757_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.172 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142111 SAMEA13540144 1701671 uncultured podovirus This sample represents an uncultured CrAss-like virus sp. provirus assembled from ERR7745759. BACPHLIP temperate score 0.18491189427312776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540144 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 12.6678 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_455_length_94197_cov_7.358882_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9863013698630136 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_455_length_94197_cov_7.358882_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.292 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; CrAss-like virus sp. virus enrichment approach none ERS11142112 SAMEA13540145 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745759. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540145 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 20.8763 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_730_length_73534_cov_12.755912_1 Viral contig found in MAG ERR7745759_bin.101 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_730_length_73534_cov_12.755912_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.1407 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142113 SAMEA13540146 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745759. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540146 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 13.4083 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1188_length_55882_cov_7.964197 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1188_length_55882_cov_7.964197 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_provirus.386 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142114 SAMEA13540147 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745759. BACPHLIP temperate score 0.01993392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540147 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 17.3453 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1543_length_47462_cov_10.069009 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9629629629629628 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1543_length_47462_cov_10.069009 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.1238 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142115 SAMEA13540148 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745759. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540148 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 17.1709 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1724_length_44410_cov_10.102655 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1724_length_44410_cov_10.102655 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.328 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1750;g__UBA7102;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3320 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142116 SAMEA13540149 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745759. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540149 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 69.1027 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1913_length_41822_cov_40.800647 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_1913_length_41822_cov_40.800647 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091217 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973;s__UMGS973 sp900547295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_provirus.500 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142117 SAMEA13540150 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745759. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540150 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 17.411 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 130 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_2121_length_39333_cov_10.365931 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_2121_length_39333_cov_10.365931 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091092 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter sp900547695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.2121 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142118 SAMEA13540151 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745759. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540151 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 56.4778 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_2343_length_36482_cov_33.645296 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_2343_length_36482_cov_33.645296 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1159 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142119 SAMEA13540152 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7745759. BACPHLIP temperate score 0.24730176211453747 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540152 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 53.5501 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_2842_length_31629_cov_32.744232 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_2842_length_31629_cov_32.744232 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_provirus.1304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142120 SAMEA13540153 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745759. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540153 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 11.357 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_3734_length_25155_cov_6.766768 Viral contig found in MAG ERR7745759_bin.79 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_3734_length_25155_cov_6.766768 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0316936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142121 SAMEA13540154 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745759. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540154 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 27.0189 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_515_length_87750_cov_15.974907 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_515_length_87750_cov_15.974907 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.515 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142123 SAMEA13540156 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745759. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540156 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 15.0311 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_908_length_65210_cov_8.790168 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6944444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_908_length_65210_cov_8.790168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.908 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142124 SAMEA13540157 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus provirus assembled from ERR7745760. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540157 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 86.7546 MAG coverage software Reads (ERR7745760) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567205) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 88 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_213_length_138085_cov_52.188706_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787374 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_213_length_138085_cov_52.188706_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME280550 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella;s__Sutterella wadsworthensis_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745760_provirus.213 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11142125 SAMEA13540158 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745760. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540158 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 21.7445 MAG coverage software Reads (ERR7745760) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567205) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 86 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_1217_length_41476_cov_13.780792 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787374 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_1217_length_41476_cov_13.780792 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738533_virus.771 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142126 SAMEA13540159 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745760. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540159 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 70.7452 MAG coverage software Reads (ERR7745760) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567205) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_1796_length_29333_cov_43.505093 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787374 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_1796_length_29333_cov_43.505093 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745777_provirus.127 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142127 SAMEA13540160 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade sp. virus assembled from ERR7745760. BACPHLIP temperate score 0.1323425218357491 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540160 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 41.426 MAG coverage software Reads (ERR7745760) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567205) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_376_length_100433_cov_25.045667 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787374 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_23_RAJ0016YZ__NODE_376_length_100433_cov_25.045667 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143505 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola dorei vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0368143 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; UAG-readthrough crAss clade sp. virus enrichment approach none ERS11142129 SAMEA13540162 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745769. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540162 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 210.791 MAG coverage software Reads (ERR7745769) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567476) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 235 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_424_length_64027_cov_130.280547_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_424_length_64027_cov_130.280547_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745769_provirus.424 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142130 SAMEA13540163 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745769. BACPHLIP temperate score 0.14641938938836815 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540163 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 79.0696 MAG coverage software Reads (ERR7745769) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567476) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_2030_length_19205_cov_46.184285 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 63.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_2030_length_19205_cov_46.184285 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143191 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__Olsenella_E sp003609875 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745769_virus.2030 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142131 SAMEA13540164 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745769. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540164 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 220.995 MAG coverage software Reads (ERR7745769) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567476) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 266 Number of CRISPR spacer hits supporting host taxonomy 595 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_724_length_44345_cov_129.011995 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_724_length_44345_cov_129.011995 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745769_virus.724 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142132 SAMEA13540165 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745769. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540165 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 10.2014 MAG coverage software Reads (ERR7745769) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567476) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_903_length_38311_cov_5.853298 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_903_length_38311_cov_5.853298 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738619_virus.1094 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142133 SAMEA13540166 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745777. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540166 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 10.842 MAG coverage software Reads (ERR7745777) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567368) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 89 Number of CRISPR spacer hits supporting host taxonomy 725 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_19_THA0061JZ__NODE_327_length_69149_cov_5.995555_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7804878048780488 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787396 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_19_THA0061JZ__NODE_327_length_69149_cov_5.995555_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0333119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142134 SAMEA13540167 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745777. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540167 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 32.5319 MAG coverage software Reads (ERR7745777) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567368) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_19_THA0061JZ__NODE_1325_length_17737_cov_18.685641 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787396 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_19_THA0061JZ__NODE_1325_length_17737_cov_18.685641 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745777_virus.1325 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142136 SAMEA13540170 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745779. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540170 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 35.6662 MAG coverage software Reads (ERR7745779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567330) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_181_length_136706_cov_20.834640_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8809523809523809 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787390 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_181_length_136706_cov_20.834640_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738451_provirus.543 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142137 SAMEA13540171 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745779. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540171 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 89.1056 MAG coverage software Reads (ERR7745779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567330) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_94_length_182926_cov_53.073503_1 Viral contig found in MAG ERR7745779_bin.159 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787390 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_94_length_182926_cov_53.073503_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745779_provirus.94 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142138 SAMEA13540172 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745779. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540172 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 53.5595 MAG coverage software Reads (ERR7745779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567330) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_1165_length_40637_cov_30.496252 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787390 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_1165_length_40637_cov_30.496252 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745779_virus.1165 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142139 SAMEA13540173 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7745779. BACPHLIP temperate score 0.3625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540173 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 9.80167 MAG coverage software Reads (ERR7745779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567330) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 470 Number of CRISPR spacer hits supporting host taxonomy 1298 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_1269_length_38168_cov_4.864404 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.525 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787390 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_1269_length_38168_cov_4.864404 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11142140 SAMEA13540174 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745779. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540174 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 15.4357 MAG coverage software Reads (ERR7745779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567330) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 87 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_223_length_121259_cov_8.683872 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5102040816326531 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787390 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_223_length_121259_cov_8.683872 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000448 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900066885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745779_virus.223 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142142 SAMEA13540176 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745779. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540176 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 53.3278 MAG coverage software Reads (ERR7745779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567330) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_776_length_56409_cov_30.274533 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787390 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_776_length_56409_cov_30.274533 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019095 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002299635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745779_virus.776 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142143 SAMEA13540177 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745783. BACPHLIP temperate score 0.04719162995594713 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540177 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 15.3994 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_1007_length_60728_cov_8.787473_1 Viral contig found in MAG ERR7745783_bin.154 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_1007_length_60728_cov_8.787473_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745783_provirus.1007 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142144 SAMEA13540178 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745783. BACPHLIP temperate score 0.3523678414096916 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540178 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 95.2315 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_218_length_137504_cov_56.899576_1 Viral contig found in MAG ERR7745783_bin.46 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9142857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_218_length_137504_cov_56.899576_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_provirus.1534 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142145 SAMEA13540179 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745783. BACPHLIP temperate score 0.28243392070484574 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540179 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 211.853 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_441_length_97722_cov_120.363726_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_441_length_97722_cov_120.363726_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_virus.854 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142146 SAMEA13540180 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745783. BACPHLIP temperate score 0.6797356828193831 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540180 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 81.3729 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_646_length_79125_cov_46.656892_1 Viral contig found in MAG ERR7745783_bin.130 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_646_length_79125_cov_46.656892_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME285832 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002300055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738263_virus.1781 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142147 SAMEA13540181 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745783. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540181 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 17.8561 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_10707_length_10301_cov_10.630086 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_10707_length_10301_cov_10.630086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745783_virus.10707 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142148 SAMEA13540182 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745783. BACPHLIP temperate score 0.05247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540182 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 55.4067 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_139_length_171720_cov_32.184587 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_139_length_171720_cov_32.184587 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME286345 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900066365 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142149 SAMEA13540183 1701671 uncultured podovirus This sample represents an uncultured Roseobacter phage CRP-7 virus assembled from ERR7745783. BACPHLIP temperate score 0.6099118942731276 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540183 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 35.1772 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_1755_length_41627_cov_20.459230 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_1755_length_41627_cov_20.459230 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738552_provirus.996 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Roseobacter phage CRP-7 virus enrichment approach none ERS11142151 SAMEA13540185 340016 uncultured virus This sample represents an uncultured Inoviridae virus assembled from ERR7745783. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540185 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 4.18477 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_27132_length_4561_cov_2.257583 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_27132_length_4561_cov_2.257583 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738185_bin.9 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745783_virus.27132 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae virus enrichment approach none ERS11142152 SAMEA13540186 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745783. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540186 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 7.11835 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 133 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_4107_length_22684_cov_3.946565 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_4107_length_22684_cov_3.946565 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_provirus.900 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142153 SAMEA13540187 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7745783. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540187 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 15.7975 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_5694_length_17422_cov_9.132257 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_5694_length_17422_cov_9.132257 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_virus.5089 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11142154 SAMEA13540188 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745783. BACPHLIP temperate score 0.5125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540188 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 147.445 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_900_length_65279_cov_82.400770 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8780487804878049 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_900_length_65279_cov_82.400770 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745783_virus.900 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142155 SAMEA13540189 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745787. BACPHLIP temperate score 0.675 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540189 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 9.38513 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1606_length_43985_cov_5.396192_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1606_length_43985_cov_5.396192_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_provirus.1606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142157 SAMEA13540191 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745787. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540191 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 10.7749 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_838_length_68409_cov_6.309723_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_838_length_68409_cov_6.309723_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_provirus.838 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142158 SAMEA13540192 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745787. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540192 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 15.6235 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1300_length_50722_cov_9.268457 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1300_length_50722_cov_9.268457 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME111561 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_virus.1300 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142159 SAMEA13540193 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745787. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540193 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 22.6836 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1576_length_44554_cov_13.471007 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1576_length_44554_cov_13.471007 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_virus.1576 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142160 SAMEA13540194 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7745787. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540194 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 243.296 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 534 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1875_length_39534_cov_143.463644 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6410256410256411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_1875_length_39534_cov_143.463644 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_virus.1875 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11142161 SAMEA13540195 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7745787. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540195 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 11.8476 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 248 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_2246_length_34294_cov_6.911068 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.53125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_2246_length_34294_cov_6.911068 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_virus.2246 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11142162 SAMEA13540196 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745787. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540196 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 8.15846 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 468 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_2815_length_28548_cov_4.635454 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_2815_length_28548_cov_4.635454 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_virus.2815 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142164 SAMEA13540198 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745787. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540198 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 23.2781 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_95_length_197729_cov_13.758191 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 26 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.6304347826086957 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_95_length_197729_cov_13.758191 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_virus.95 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142165 SAMEA13540199 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745815. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540199 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 109.716 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_1246_length_52590_cov_64.338107_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_1246_length_52590_cov_64.338107_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_provirus.1246 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142166 SAMEA13540200 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745815. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540200 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 110.736 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2012 Number of CRISPR spacer hits supporting host taxonomy 393 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_162_length_146826_cov_64.445291_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_162_length_146826_cov_64.445291_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_provirus.162 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142167 SAMEA13540201 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745815. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540201 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 43.9181 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_2722_length_31646_cov_30.142830_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_2722_length_31646_cov_30.142830_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_virus.2830 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142168 SAMEA13540202 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745815. BACPHLIP temperate score 0.425 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540202 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 16.4883 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 272 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_533_length_83976_cov_9.732273_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_533_length_83976_cov_9.732273_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_virus.391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142170 SAMEA13540204 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745815. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540204 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 29.017 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 248 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_1193_length_53887_cov_16.730069 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.59375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_1193_length_53887_cov_16.730069 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142171 SAMEA13540205 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745815. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540205 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 18.1956 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 73 Number of CRISPR spacer hits supporting host taxonomy 268 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_1639_length_44317_cov_10.641817 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_1639_length_44317_cov_10.641817 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.1407 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142172 SAMEA13540206 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745815. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540206 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 21.1025 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 64 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_199_length_137122_cov_12.050969 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_199_length_137122_cov_12.050969 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.199 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142173 SAMEA13540207 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745815. BACPHLIP temperate score 0.11497797356828196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540207 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 47.5405 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 518 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_2183_length_36651_cov_33.717805 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_2183_length_36651_cov_33.717805 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142174 SAMEA13540208 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7745815. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540208 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 7.18395 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_23675_length_5260_cov_3.892533 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_23675_length_5260_cov_3.892533 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738530_bin.33 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium sp900539945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0010187 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11142175 SAMEA13540209 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745815. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540209 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 33.1863 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_2890_length_30333_cov_18.891955 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_2890_length_30333_cov_18.891955 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738555_provirus.57 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142176 SAMEA13540210 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745815. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540210 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 23.6042 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 190 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_3858_length_24324_cov_14.404091 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_3858_length_24324_cov_14.404091 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.2093 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142177 SAMEA13540211 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745815. BACPHLIP temperate score 0.05927917672702029 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540211 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 16.3758 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_4620_length_21117_cov_9.431939 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_4620_length_21117_cov_9.431939 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000818 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A;s__Mediterraneibacter_A butyricigenes vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.4620 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142179 SAMEA13540213 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745815. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540213 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 36.0529 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 81 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_960_length_61115_cov_20.622186 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6551724137931034 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_960_length_61115_cov_20.622186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745545_virus.467 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142180 SAMEA13540214 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745816. BACPHLIP temperate score 0.07725770925110134 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540214 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 200.673 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_1742_length_35026_cov_114.780852_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_1742_length_35026_cov_114.780852_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.4060 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142181 SAMEA13540215 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745816. BACPHLIP temperate score 0.16238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540215 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 15.705 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_447_length_90888_cov_8.788186_1 Viral contig found in MAG ERR7745816_bin.238 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_447_length_90888_cov_8.788186_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.2157 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142182 SAMEA13540216 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745816. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540216 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 19.9252 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 101 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_1026_length_52457_cov_11.111798 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_1026_length_52457_cov_11.111798 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738219_virus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142183 SAMEA13540217 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745816. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540217 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 172.762 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_1295_length_43517_cov_98.031860 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.55 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_1295_length_43517_cov_98.031860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745924_bin.93 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__Firm-10;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.3571550 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142185 SAMEA13540219 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745816. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540219 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 10.8252 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 420 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_1699_length_35750_cov_5.972612 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_1699_length_35750_cov_5.972612 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.865 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142186 SAMEA13540220 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745816. BACPHLIP temperate score 0.14975453690774357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540220 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 14.5725 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_2116_length_29990_cov_8.211781 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_2116_length_29990_cov_8.211781 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745594_bin.118 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;s__UBA636 sp900546285 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1081591 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142187 SAMEA13540221 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7745816. BACPHLIP temperate score 0.03799472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540221 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 503.812 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_350_length_104493_cov_282.803555 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9850746268656716 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_350_length_104493_cov_282.803555 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0369190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11142188 SAMEA13540222 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745816. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540222 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 41.9124 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 141 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_711_length_66617_cov_23.545582 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_711_length_66617_cov_23.545582 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142189 SAMEA13540223 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745819. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540223 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 8.67055 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_1164_length_49909_cov_5.061266_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_1164_length_49909_cov_5.061266_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747255_bin.83 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-884;s__CAG-884 sp000433875 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_provirus.1164 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142190 SAMEA13540224 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7745819. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540224 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 97.3588 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1030 Number of CRISPR spacer hits supporting host taxonomy 119 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_178_length_139561_cov_58.871699_1 Viral contig found in MAG ERR7745819_bin.108 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4482758620689655 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_178_length_139561_cov_58.871699_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME286345 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900066365 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738268_virus.1266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11142191 SAMEA13540225 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745819. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540225 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 421.651 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_553_length_76825_cov_250.192161_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_553_length_76825_cov_250.192161_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_provirus.553 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142193 SAMEA13540227 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745819. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540227 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 7.4108 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 214 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_1636_length_39953_cov_4.148861 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_1636_length_39953_cov_4.148861 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1636 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142194 SAMEA13540228 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7745819. BACPHLIP temperate score 0.10236784140969162 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540228 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 46.8718 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_2143_length_32934_cov_29.029004 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_2143_length_32934_cov_29.029004 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_provirus.1304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142195 SAMEA13540229 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745819. BACPHLIP temperate score 0.19741189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540229 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 7.83556 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_3693_length_21440_cov_4.577353 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_3693_length_21440_cov_4.577353 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738227_bin.197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp004557855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745410_virus.1183 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142196 SAMEA13540230 2100421 uncultured Caudovirales phage This sample represents an uncultured Schitoviridae virus assembled from ERR7745819. BACPHLIP temperate score 0.06303277487972782 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540230 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 20.6681 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 324 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_596_length_73968_cov_12.564318 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_596_length_73968_cov_12.564318 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738189_virus.309 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Schitoviridae virus enrichment approach none ERS11142197 SAMEA13540231 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745823. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540231 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 17.0404 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_1466_length_51893_cov_9.575807_1 Viral contig found in MAG ERR7745823_bin.236 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_1466_length_51893_cov_9.575807_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_provirus.1466 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142199 SAMEA13540233 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745823. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540233 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 39.1141 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_360_length_115057_cov_24.262280_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3235294117647059 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_360_length_115057_cov_24.262280_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_provirus.360 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142200 SAMEA13540234 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745823. BACPHLIP temperate score 0.3875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540234 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 28.3118 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_566_length_90825_cov_16.494898_1 Viral contig found in MAG ERR7745823_bin.124 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_566_length_90825_cov_16.494898_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_provirus.566 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142201 SAMEA13540235 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745823. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540235 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 13.7912 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_751_length_77485_cov_7.834901_1 Viral contig found in MAG ERR7745823_bin.25 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_751_length_77485_cov_7.834901_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME110833 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;s__COE1 sp900753305 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_provirus.751 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142202 SAMEA13540236 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745823. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540236 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 19.4662 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_1064_length_63454_cov_11.110087 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_1064_length_63454_cov_11.110087 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0347918 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142203 SAMEA13540237 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7745823. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540237 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 11.0453 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_1480_length_51558_cov_6.142791 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6590909090909091 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_1480_length_51558_cov_6.142791 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11142204 SAMEA13540238 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745823. BACPHLIP temperate score 0.16375920696193652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540238 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 22.7813 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_2039_length_41232_cov_13.249812 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_2039_length_41232_cov_13.249812 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142205 SAMEA13540239 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745823. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540239 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 12.2189 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_2437_length_36583_cov_6.892429 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_2437_length_36583_cov_6.892429 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_virus.2437 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142206 SAMEA13540240 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7745823. BACPHLIP temperate score 0.06798872201629169 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540240 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 11.5636 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_27966_length_5558_cov_6.601168 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_27966_length_5558_cov_6.601168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_virus.27966 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11142208 SAMEA13540242 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745823. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540242 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 10.8395 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_5560_length_20471_cov_6.070315 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_5560_length_20471_cov_6.070315 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_virus.1931 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142209 SAMEA13540243 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745823. BACPHLIP temperate score 0.02984581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540243 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 21.3267 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_9104_length_14155_cov_12.190767 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_9104_length_14155_cov_12.190767 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_virus.9104 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142210 SAMEA13540244 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7745828. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540244 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 249.289 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_221_length_112949_cov_137.398823_1 Viral contig found in MAG ERR7745828_bin.59 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_221_length_112949_cov_137.398823_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_provirus.221 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142211 SAMEA13540245 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745828. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540245 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 105.587 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_516_length_74676_cov_62.125605_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.48484848484848486 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_516_length_74676_cov_62.125605_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_provirus.516 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142212 SAMEA13540246 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745828. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540246 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 306.366 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_861_length_55530_cov_168.583142_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_861_length_55530_cov_168.583142_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_provirus.363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142214 SAMEA13540248 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745828. BACPHLIP temperate score 0.0752082847671273 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540248 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 24.688 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_1982_length_30929_cov_14.808829 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_1982_length_30929_cov_14.808829 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.2075 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142215 SAMEA13540249 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7745828. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540249 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 15.3415 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 226 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_279_length_102194_cov_17.296924 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5813953488372093 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_279_length_102194_cov_17.296924 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11142216 SAMEA13540250 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745828. BACPHLIP temperate score 0.18068787764054067 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540250 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 11.5783 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_4150_length_16540_cov_6.407398 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_4150_length_16540_cov_6.407398 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.4150 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142217 SAMEA13540251 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745828. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540251 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 79.6801 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_821_length_57359_cov_45.704305 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_821_length_57359_cov_45.704305 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.821 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142218 SAMEA13540252 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7745831. BACPHLIP temperate score 0.11873985389093908 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540252 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 21.9796 MAG coverage software Reads (ERR7745831) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567123) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_190_length_98825_cov_12.673178_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787341 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_190_length_98825_cov_12.673178_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142219 SAMEA13540253 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745831. BACPHLIP temperate score 0.9061536050499776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540253 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 30.427 MAG coverage software Reads (ERR7745831) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567123) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_716_length_48864_cov_18.903806_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787341 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_716_length_48864_cov_18.903806_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738353_virus.937 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142220 SAMEA13540254 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745831. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540254 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 70.5654 MAG coverage software Reads (ERR7745831) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567123) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_1240_length_34620_cov_40.811366 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7941176470588235 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787341 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_1240_length_34620_cov_40.811366 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R;s__Eubacterium_R sp900542875 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_virus.1240 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142222 SAMEA13540256 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745831. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540256 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 78.2589 MAG coverage software Reads (ERR7745831) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567123) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 191 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_807_length_45704_cov_45.386723 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787341 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_807_length_45704_cov_45.386723 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_virus.1079 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142223 SAMEA13540257 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745835. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540257 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 20.1145 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 737 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_1053_length_53311_cov_12.072416_1 Viral contig found in MAG ERR7745835_bin.12 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_1053_length_53311_cov_12.072416_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0278013 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142224 SAMEA13540258 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7745835. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540258 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 12.5493 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 71 Number of CRISPR spacer hits supporting host taxonomy 280 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_188_length_131701_cov_7.565148_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.6274509803921569 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_188_length_131701_cov_7.565148_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_provirus.188 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142225 SAMEA13540259 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745835. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540259 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 28.8758 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 226 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_495_length_81458_cov_17.173407_1 Viral contig found in MAG ERR7745835_bin.67 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_495_length_81458_cov_17.173407_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_provirus.495 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142226 SAMEA13540260 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745835. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540260 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 21.3707 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_86_length_182266_cov_12.567510_1 Viral contig found in MAG ERR7745835_bin.185 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7037037037037037 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_86_length_182266_cov_12.567510_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_provirus.1146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142228 SAMEA13540262 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745835. BACPHLIP temperate score 0.07834114492378066 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540262 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 21.8748 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 108 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_1741_length_39405_cov_13.170718 Viral contig found in MAG ERR7745835_bin.87 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_1741_length_39405_cov_13.170718 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268665 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus thermophilus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_virus.1741 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142229 SAMEA13540263 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745835. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540263 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 9.32079 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_2076_length_34855_cov_5.109149 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_2076_length_34855_cov_5.109149 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.1250 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142230 SAMEA13540264 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7745835. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540264 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 11.9936 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 801 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_2827_length_27385_cov_7.046397 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_2827_length_27385_cov_7.046397 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0299347 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11142231 SAMEA13540265 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745835. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540265 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 114.353 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_533_length_78077_cov_68.699397 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.912280701754386 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_533_length_78077_cov_68.699397 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_virus.533 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142232 SAMEA13540266 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745835. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540266 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 223.031 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_980_length_55850_cov_136.395801 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_980_length_55850_cov_136.395801 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_virus.1999 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142233 SAMEA13540267 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745836. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540267 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 60.6878 MAG coverage software Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 129 Number of CRISPR spacer hits supporting host taxonomy 82 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_153_length_117008_cov_34.156571_1 Viral contig found in MAG ERR7745836_bin.46 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787340 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_153_length_117008_cov_34.156571_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738599_virus.1890 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142234 SAMEA13540268 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745836. BACPHLIP temperate score 0.129625550660793 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540268 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 21.3672 MAG coverage software Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_353_length_73311_cov_14.652757_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787340 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_353_length_73311_cov_14.652757_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745836_provirus.353 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142235 SAMEA13540269 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745836. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540269 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 23.1012 MAG coverage software Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_770_length_45991_cov_12.816243_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787340 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_770_length_45991_cov_12.816243_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745836_provirus.770 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142237 SAMEA13540271 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7745836. BACPHLIP temperate score 0.11416849755093 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540271 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 126.646 MAG coverage software Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_210_length_96420_cov_70.798086 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.9315068493150684 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787340 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_210_length_96420_cov_70.798086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11142238 SAMEA13540272 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745836. BACPHLIP temperate score 0.20722793596202008 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540272 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 115.569 MAG coverage software Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 79 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_569_length_55452_cov_66.593156 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787340 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_569_length_55452_cov_66.593156 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738619_provirus.454 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142239 SAMEA13540273 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745836. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540273 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 23.4852 MAG coverage software Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_923_length_40842_cov_13.113112 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787340 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_923_length_40842_cov_13.113112 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745836_virus.923 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142240 SAMEA13540274 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu provirus assembled from ERR7745845. BACPHLIP temperate score 0.25195538818076474 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540274 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 48.4369 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1465_length_52166_cov_27.756091_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1465_length_52166_cov_27.756091_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_provirus.1465 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11142241 SAMEA13540275 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745845. BACPHLIP temperate score 0.10290470637156364 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540275 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 16.0367 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_217_length_145508_cov_9.026851_1 Viral contig found in MAG ERR7745845_bin.42 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_217_length_145508_cov_9.026851_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_provirus.2338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142243 SAMEA13540277 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745845. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540277 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 12.3884 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_850_length_72917_cov_7.001840_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_850_length_72917_cov_7.001840_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738151_bin.225 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter sp900548765 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_provirus.850 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142244 SAMEA13540278 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745845. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540278 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 18.5031 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1098_length_61864_cov_10.674851 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1098_length_61864_cov_10.674851 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0339891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142245 SAMEA13540279 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745845. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540279 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 47.8037 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 143 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1274_length_57114_cov_28.064555 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1274_length_57114_cov_28.064555 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142246 SAMEA13540280 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745845. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540280 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 50.6991 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1593_length_49375_cov_28.576900 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1593_length_49375_cov_28.576900 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900542795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.2014 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142247 SAMEA13540281 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745845. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540281 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 16.1715 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 277 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1935_length_43517_cov_10.072629 Viral contig found in MAG ERR7745845_bin.4 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_1935_length_43517_cov_10.072629 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142248 SAMEA13540282 926697 uncultured Microviridae This sample represents an uncultured unclassified Microviridae virus assembled from ERR7745845. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540282 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 5.42005 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_22137_length_5178_cov_3.226034 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_22137_length_5178_cov_3.226034 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME153344 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900549705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.23843 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae virus enrichment approach none ERS11142249 SAMEA13540283 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745845. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540283 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 11.5181 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_2388_length_37452_cov_6.448107 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_2388_length_37452_cov_6.448107 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME285832 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002300055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.1352 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142251 SAMEA13540285 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745845. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540285 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 133.212 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 80 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_465_length_101971_cov_77.212378 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.4838709677419355 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_465_length_101971_cov_77.212378 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME172369 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-917;g__CAG-349;s__CAG-349 sp003539515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.593 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142252 SAMEA13540286 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745845. BACPHLIP temperate score 0.05011329479852357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540286 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 20.1505 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 64 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_6807_length_16174_cov_11.674722 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_6807_length_16174_cov_11.674722 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME239799 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella;s__Eisenbergiella sp900066775 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.7813 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142253 SAMEA13540287 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745852. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540287 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 82.5418 MAG coverage software Reads (ERR7745852) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560337) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-E-H_O_23_1813__NODE_203_length_116847_cov_50.470455_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586013 sample name Hadza_MoBio_hadza-E-H_O_23_1813__NODE_203_length_116847_cov_50.470455_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745852_provirus.203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142254 SAMEA13540288 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745852. BACPHLIP temperate score 0.12525657272474092 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540288 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 1598.53 MAG coverage software Reads (ERR7745852) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560337) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 379 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_O_23_1813__NODE_762_length_43084_cov_924.106122_1 Viral contig found in MAG ERR7745852_bin.80 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47368421052631576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586013 sample name Hadza_MoBio_hadza-E-H_O_23_1813__NODE_762_length_43084_cov_924.106122_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143357 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides ovatus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0322078 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142255 SAMEA13540289 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745852. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540289 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 2557.68 MAG coverage software Reads (ERR7745852) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560337) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_O_23_1813__NODE_532_length_59181_cov_1469.854240 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.32142857142857145 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586013 sample name Hadza_MoBio_hadza-E-H_O_23_1813__NODE_532_length_59181_cov_1469.854240 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143357 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides ovatus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745852_virus.532 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142257 SAMEA13540291 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745854. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540291 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 198.85 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_171_length_161602_cov_121.874744_1 Viral contig found in MAG ERR7745854_bin.346 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_171_length_161602_cov_121.874744_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745625_provirus.431 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142258 SAMEA13540292 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745854. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540292 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 13.696 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_248_length_137943_cov_7.944272_1 Viral contig found in MAG ERR7745854_bin.180 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.5161290322580645 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_248_length_137943_cov_7.944272_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.863 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142259 SAMEA13540293 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745854. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540293 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 21.4311 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_379_length_112480_cov_13.035497_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_379_length_112480_cov_13.035497_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738606_virus.1947 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142260 SAMEA13540294 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745854. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540294 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 13.8984 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_786_length_79151_cov_8.485381_1 Viral contig found in MAG ERR7745854_bin.304 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_786_length_79151_cov_8.485381_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_provirus.786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142261 SAMEA13540295 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745854. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540295 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 60.0794 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_1111_length_64239_cov_71.172641 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_1111_length_64239_cov_71.172641 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_virus.1111 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142262 SAMEA13540296 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745854. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540296 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 11.1737 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_1366_length_57031_cov_6.586017 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_1366_length_57031_cov_6.586017 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME013942 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724;s__CAG-724 sp003524145 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745398_virus.695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142263 SAMEA13540297 1701671 uncultured podovirus This sample represents an uncultured Paenibacillus phage vB_PlaP_API480 virus assembled from ERR7745854. BACPHLIP temperate score 0.2023678414096917 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540297 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 9.18969 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_1887_length_45434_cov_5.319576 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_1887_length_45434_cov_5.319576 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746285_bin.189 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.831 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Paenibacillus phage vB_PlaP_API480 virus enrichment approach none ERS11142264 SAMEA13540298 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745854. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540298 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 12.832 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_2185_length_41326_cov_7.654780 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_2185_length_41326_cov_7.654780 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.971 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142266 SAMEA13540300 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745854. BACPHLIP temperate score 0.3368672824538925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540300 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 8.56061 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_2756_length_34882_cov_4.809252 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; HMM-based (lower-bound) completeness score 52.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_2756_length_34882_cov_4.809252 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1636 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142267 SAMEA13540301 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745854. BACPHLIP temperate score 0.06384348183251046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540301 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 26.0708 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 155 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_3244_length_31217_cov_16.618433 Viral contig found in MAG ERR7745854_bin.125 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_3244_length_31217_cov_16.618433 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142268 SAMEA13540302 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7745854. BACPHLIP temperate score 0.12878892628021937 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540302 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 17.0748 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_495_length_98774_cov_10.024519 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_495_length_98774_cov_10.024519 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746012_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11142269 SAMEA13540303 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745854. BACPHLIP temperate score 0.06574293217546884 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540303 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 7.22254 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_6623_length_18097_cov_4.091176 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_6623_length_18097_cov_4.091176 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745429_provirus.538 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142270 SAMEA13540304 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745854. BACPHLIP temperate score 0.01996515875021345 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540304 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 47.177 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_9842_length_13262_cov_28.392188 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_9842_length_13262_cov_28.392188 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_virus.5711 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142272 SAMEA13540306 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745858. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540306 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 45.7879 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_2360_length_36729_cov_26.450344_1 Viral contig found in MAG ERR7745858_bin.243 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_2360_length_36729_cov_26.450344_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745908_bin.180 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820;s__UMGS1820 sp902797885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745858_provirus.2360 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142273 SAMEA13540307 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745858. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540307 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 83.5088 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_522_length_102177_cov_48.527767_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_522_length_102177_cov_48.527767_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0344636 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142274 SAMEA13540308 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745858. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540308 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 83.2597 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_930_length_69961_cov_51.673788_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_930_length_69961_cov_51.673788_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.386 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142275 SAMEA13540309 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745858. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540309 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 13.2569 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_1490_length_51193_cov_7.384557 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_1490_length_51193_cov_7.384557 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745858_virus.1490 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142276 SAMEA13540310 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745858. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540310 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 3385.01 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 440 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_1787_length_44682_cov_1863.908082 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_1787_length_44682_cov_1863.908082 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.38 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp003525905 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745858_virus.1787 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142277 SAMEA13540311 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745858. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540311 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 20.245 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_2001_length_41147_cov_11.332968 Viral contig found in MAG ERR7745858_bin.67 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_2001_length_41147_cov_11.332968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.329 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__UBA1191 sp900549125 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738272_virus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142279 SAMEA13540313 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745858. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540313 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 7.5458 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_3652_length_26233_cov_4.050314 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_3652_length_26233_cov_4.050314 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME255646 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900552475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_virus.2039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142280 SAMEA13540314 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745858. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540314 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 50.0011 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_931_length_69954_cov_28.332670 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.4897959183673469 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_931_length_69954_cov_28.332670 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380017 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142281 SAMEA13540315 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745859. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540315 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 12.6919 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_1622_length_54415_cov_7.494093_1 Viral contig found in MAG ERR7745859_bin.219 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_1622_length_54415_cov_7.494093_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142085 SAMEA13540118 1478972 Gokushovirinae environmental samples This sample represents an uncultured Gokushovirus WZ-2015a virus assembled from ERR7745719. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540118 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:46Z INSDC last update 2022-12-27T01:22:46Z INSDC status public MAG coverage depth 12.2825 MAG coverage software Reads (ERR7745719) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559922) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 263 Number of CRISPR spacer hits supporting host taxonomy 138 Submitter Id Hadza_MoBio_hadza-I-L_M_5_2492__NODE_5992_length_14643_cov_10.744817 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586266 sample name Hadza_MoBio_hadza-I-L_M_5_2492__NODE_5992_length_14643_cov_10.744817 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.5992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; unclassified Gokushovirinae; Gokushovirus WZ-2015a virus enrichment approach none ERS11142122 SAMEA13540155 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745759. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540155 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 38.6084 MAG coverage software Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_A_10_1110__NODE_6533_length_15873_cov_23.130031 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585534 sample name Hadza_MoBio_hadza-A-D_A_10_1110__NODE_6533_length_15873_cov_23.130031 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.6533 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142128 SAMEA13540161 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745769. BACPHLIP temperate score 0.174534272590563 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540161 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 190.738 MAG coverage software Reads (ERR7745769) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567476) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_148_length_117735_cov_113.807042_1 Viral contig found in MAG ERR7745769_bin.49 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787407 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_1_THA1067YZ__NODE_148_length_117735_cov_113.807042_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0332956 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142135 SAMEA13540169 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745777. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540169 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 23.3202 MAG coverage software Reads (ERR7745777) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567368) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 231 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_19_THA0061JZ__NODE_719_length_35189_cov_13.350308 Viral contig found in MAG ERR7745777_bin.35 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787396 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_19_THA0061JZ__NODE_719_length_35189_cov_13.350308 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142141 SAMEA13540175 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745779. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540175 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 219.048 MAG coverage software Reads (ERR7745779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567330) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 101 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_505_length_73784_cov_123.910036 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787390 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_17_RAU1014YZ__NODE_505_length_73784_cov_123.910036 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745779_virus.505 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142150 SAMEA13540184 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745783. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540184 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 40.089 MAG coverage software Reads (ERR7745783) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559670) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_L_24_2330__NODE_2189_length_36059_cov_22.629037 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586200 sample name Hadza_MoBio_hadza-E-H_L_24_2330__NODE_2189_length_36059_cov_22.629037 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738604_bin.142 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432655 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738217_provirus.242 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142156 SAMEA13540190 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745787. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540190 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 165.508 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 139 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_274_length_127889_cov_101.863557_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.40540540540540543 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_274_length_127889_cov_101.863557_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745787_provirus.274 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142163 SAMEA13540197 2133760 Siphoviridae environmental samples This sample represents an uncultured Cequinquevirus virus assembled from ERR7745787. BACPHLIP temperate score 0.275 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540197 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 34.4236 MAG coverage software Reads (ERR7745787) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 201 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_3943_length_21493_cov_20.459703 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787337 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_7_CHE0004BZ__NODE_3943_length_21493_cov_20.459703 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738558_virus.1847 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Cequinquevirus virus enrichment approach none ERS11142169 SAMEA13540203 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745815. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540203 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:45Z INSDC last update 2022-12-27T01:22:45Z INSDC status public MAG coverage depth 10.5797 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 82 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_925_length_62489_cov_6.130616_1 Viral contig found in MAG ERR7745815_bin.112 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 78.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.56 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_925_length_62489_cov_6.130616_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140296 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__TF01-11 sp003529475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_provirus.925 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142178 SAMEA13540212 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745815. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540212 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 13.606 MAG coverage software Reads (ERR7745815) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567746) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 197 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_805_length_67488_cov_7.991455 Viral contig found in MAG ERR7745815_bin.72 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585898 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_22_1655__NODE_805_length_67488_cov_7.991455 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745815_virus.805 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142184 SAMEA13540218 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745816. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540218 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 24.9058 MAG coverage software Reads (ERR7745816) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561185) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_G_11_1585__NODE_1425_length_40826_cov_15.143734 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585834 sample name Hadza_MoBio_C-REDO_G_11_1585__NODE_1425_length_40826_cov_15.143734 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.1121 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142192 SAMEA13540226 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745819. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540226 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 20.1646 MAG coverage software Reads (ERR7745819) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559689) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 42 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_N_20_2340__NODE_1097_length_51891_cov_12.279287 Viral contig found in MAG ERR7745819_bin.35 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8484848484848485 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586210 sample name Hadza_MoBio_hadza-E-H_N_20_2340__NODE_1097_length_51891_cov_12.279287 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746111_bin.94 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.1348 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142198 SAMEA13540232 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745823. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540232 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:44Z INSDC last update 2022-12-27T01:22:44Z INSDC status public MAG coverage depth 31.5482 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_20_length_364120_cov_17.950761_1 Viral contig found in MAG ERR7745823_bin.344 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_20_length_364120_cov_17.950761_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738240_bin.221 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R;s__Eubacterium_R sp900539325 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.13 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142207 SAMEA13540241 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745823. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540241 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 7.33039 MAG coverage software Reads (ERR7745823) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559376) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_G_18_2610__NODE_40678_length_4006_cov_4.111733 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586320 sample name Hadza_MoBio_hadza-I-L_G_18_2610__NODE_40678_length_4006_cov_4.111733 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745823_virus.40678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142213 SAMEA13540247 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745828. BACPHLIP temperate score 0.2099118942731278 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540247 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 38.6845 MAG coverage software Reads (ERR7745828) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560377) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 108 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-E-H_A_2_1814__NODE_1269_length_43058_cov_22.554640 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-24 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586014 sample name Hadza_MoBio_hadza-E-H_A_2_1814__NODE_1269_length_43058_cov_22.554640 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.1269 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142221 SAMEA13540255 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745831. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540255 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 10.7133 MAG coverage software Reads (ERR7745831) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567123) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_40_length_199900_cov_6.113736 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; HMM-based (lower-bound) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 17 number of unique standard tRNAs extracted 12 percent of BLAST hits supporting viral taxonomy 0.9642857142857144 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787341 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_13_CHE0012SZ__NODE_40_length_199900_cov_6.113736 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_virus.40 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142227 SAMEA13540261 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745835. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540261 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:43Z INSDC last update 2022-12-27T01:22:43Z INSDC status public MAG coverage depth 36.4249 MAG coverage software Reads (ERR7745835) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560711) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_E_9_1723__NODE_1424_length_44820_cov_22.124735 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585966 sample name Hadza_MoBio_hadza-E-H_E_9_1723__NODE_1424_length_44820_cov_22.124735 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.1026 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142236 SAMEA13540270 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745836. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540270 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 7.70954 MAG coverage software Reads (ERR7745836) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567121) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 131 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_1272_length_32533_cov_4.021691 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787340 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_9_CHE0010BZ__NODE_1272_length_32533_cov_4.021691 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745836_virus.1272 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142242 SAMEA13540276 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe provirus assembled from ERR7745845. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540276 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 22.3762 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 221 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_471_length_101148_cov_13.573280_1 Viral contig found in MAG ERR7745845_bin.169 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9836065573770492 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_471_length_101148_cov_13.573280_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372952 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11142250 SAMEA13540284 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745845. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540284 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 67.2478 MAG coverage software Reads (ERR7745845) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559413) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_K_18_2626__NODE_2990_length_31854_cov_37.740315 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586335 sample name Hadza_MoBio_hadza-I-L_K_18_2626__NODE_2990_length_31854_cov_37.740315 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745594_bin.118 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;s__UBA636 sp900546285 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_virus.2990 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142256 SAMEA13540290 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. provirus assembled from ERR7745854. BACPHLIP temperate score 0.15966643118087134 ENA-FIRST-PUBLIC 2022-12-27T01:22:42Z ENA-LAST-UPDATE 2022-12-27T01:22:42Z External Id SAMEA13540290 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 6.3563 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_11962_length_11357_cov_3.505319_1 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_11962_length_11357_cov_3.505319_1 scientific_name uncultured Microviridae sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME022295 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus sp900544435 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_provirus.4601 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. ERS11142265 SAMEA13540299 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745854. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540299 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 17.6801 MAG coverage software Reads (ERR7745854) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567859) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_247_length_138006_cov_10.646782 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 20 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.5471698113207547 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585786 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_10_1531__NODE_247_length_138006_cov_10.646782 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0374893 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142271 SAMEA13540305 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745858. BACPHLIP temperate score 0.15462555066079303 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540305 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 97.7395 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 122 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_1485_length_51335_cov_55.796832_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_1485_length_51335_cov_55.796832_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098563 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;s__Roseburia sp900552665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745858_provirus.1485 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142278 SAMEA13540312 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745858. BACPHLIP temperate score 0.827477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540312 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 52.4109 MAG coverage software Reads (ERR7745858) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567238) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 596 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_2529_length_34965_cov_29.473573 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 77.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787377 sample name Nepal_MoBio_Fiber-Hadza-Nepal_H_19_RAJ0022YZ__NODE_2529_length_34965_cov_29.473573 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142282 SAMEA13540316 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745859. BACPHLIP temperate score 0.06941133531732865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540316 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 43.9723 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 224 Number of CRISPR spacer hits supporting host taxonomy 156 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2477_length_39651_cov_28.467302_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2477_length_39651_cov_28.467302_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0226686 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142283 SAMEA13540317 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745859. BACPHLIP temperate score 0.25194340863071135 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540317 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 57.2624 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_5018_length_23724_cov_37.115956_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_5018_length_23724_cov_37.115956_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.2612 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142284 SAMEA13540318 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745859. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540318 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 28.7935 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 259 Number of CRISPR spacer hits supporting host taxonomy 288 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_998_length_74974_cov_17.471875_1 Viral contig found in MAG ERR7745859_bin.80 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_998_length_74974_cov_17.471875_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME176098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_provirus.776 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142285 SAMEA13540319 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745859. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540319 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 31.9583 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 445 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_1264_length_63924_cov_19.209391 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.9696969696969696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_1264_length_63924_cov_19.209391 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745859_virus.1264 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142286 SAMEA13540320 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7745859. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540320 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 19.5399 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_14343_length_9981_cov_11.503534 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 84.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_14343_length_9981_cov_11.503534 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.10555 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11142287 SAMEA13540321 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745859. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540321 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 41.7445 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_1554_length_55962_cov_24.594936 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_1554_length_55962_cov_24.594936 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.1503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142288 SAMEA13540322 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745859. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540322 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 10.0099 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_18737_length_7937_cov_5.784733 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_18737_length_7937_cov_5.784733 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738227_bin.197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp004557855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745859_virus.18737 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142289 SAMEA13540323 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745859. BACPHLIP temperate score 0.06347739359623317 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540323 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 9.5601 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2135_length_44017_cov_5.513314 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2135_length_44017_cov_5.513314 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME010079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.1020 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142290 SAMEA13540324 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745859. BACPHLIP temperate score 0.57695538818076475 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540324 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 15.4858 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 99 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2459_length_39827_cov_9.366692 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 90.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5925925925925926 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2459_length_39827_cov_9.366692 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737966_provirus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142291 SAMEA13540325 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745859. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540325 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 23.8696 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2746_length_37269_cov_14.223677 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_2746_length_37269_cov_14.223677 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.2480 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142292 SAMEA13540326 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745859. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540326 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 14.9136 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_314_length_135267_cov_8.810874 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 25 number of unique standard tRNAs extracted 20 percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_314_length_135267_cov_8.810874 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745859_virus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142293 SAMEA13540327 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745859. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540327 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 168.163 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 78 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_3728_length_29777_cov_101.118889 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_3728_length_29777_cov_101.118889 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.2034 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142294 SAMEA13540328 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745859. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540328 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 18.9347 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 155 Number of CRISPR spacer hits supporting host taxonomy 965 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_4589_length_25483_cov_11.249154 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.72 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_4589_length_25483_cov_11.249154 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738145_provirus.803 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142295 SAMEA13540329 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745859. BACPHLIP temperate score 0.13727973568281945 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13540329 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-28T19:46:20Z INSDC status public MAG coverage depth 16.2858 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_5318_length_22654_cov_9.352748 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_5318_length_22654_cov_9.352748 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738661_bin.249 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.4692 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142296 SAMEA13540330 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr130_1 virus assembled from ERR7745859. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540330 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 291.748 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_617_length_97742_cov_173.653909 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7628865979381443 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_617_length_97742_cov_173.653909 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268072 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella stercorea vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.211 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr130_1 virus enrichment approach none ERS11142297 SAMEA13540331 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745859. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540331 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 46.4556 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_7789_length_16618_cov_27.447131 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 55.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_7789_length_16618_cov_27.447131 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.6784 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142298 SAMEA13540332 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745859. BACPHLIP temperate score 0.575 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540332 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:42Z INSDC last update 2022-12-27T01:22:42Z INSDC status public MAG coverage depth 11.6198 MAG coverage software Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_9383_length_14199_cov_6.959992 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166__NODE_9383_length_14199_cov_6.959992 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.8602 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142299 SAMEA13540333 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745867. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540333 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 9.26396 MAG coverage software Reads (ERR7745867) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559896) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_K_21_2489__NODE_334_length_92320_cov_5.199115_1 Viral contig found in MAG ERR7745867_bin.36 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586263 sample name Hadza_MoBio_hadza-I-L_K_21_2489__NODE_334_length_92320_cov_5.199115_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME233621 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D;s__Ruminococcus_D sp000434695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_provirus.88 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142300 SAMEA13540334 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745867. BACPHLIP temperate score 0.852477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540334 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 27.9648 MAG coverage software Reads (ERR7745867) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559896) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_hadza-I-L_K_21_2489__NODE_612_length_67753_cov_16.263240_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586263 sample name Hadza_MoBio_hadza-I-L_K_21_2489__NODE_612_length_67753_cov_16.263240_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_provirus.117 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142301 SAMEA13540335 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745867. BACPHLIP temperate score 0.03995011113590989 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540335 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 10.742 MAG coverage software Reads (ERR7745867) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559896) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_K_21_2489__NODE_1213_length_43549_cov_5.885305 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586263 sample name Hadza_MoBio_hadza-I-L_K_21_2489__NODE_1213_length_43549_cov_5.885305 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738157_bin.149 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.1038 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142302 SAMEA13540336 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745867. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540336 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 21.2837 MAG coverage software Reads (ERR7745867) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559896) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-I-L_K_21_2489__NODE_1475_length_37514_cov_12.272431 Viral contig found in MAG ERR7745867_bin.77 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586263 sample name Hadza_MoBio_hadza-I-L_K_21_2489__NODE_1475_length_37514_cov_12.272431 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME006546 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-605;s__CAG-605 sp000433255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745366_provirus.22 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142303 SAMEA13540337 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745867. BACPHLIP temperate score 0.12241189427312776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540337 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 7.89861 MAG coverage software Reads (ERR7745867) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559896) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_K_21_2489__NODE_2450_length_24876_cov_4.343159 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586263 sample name Hadza_MoBio_hadza-I-L_K_21_2489__NODE_2450_length_24876_cov_4.343159 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__MARSEILLE-P3954;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745719_virus.1568 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142304 SAMEA13540338 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745867. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540338 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 12.924 MAG coverage software Reads (ERR7745867) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559896) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-I-L_K_21_2489__NODE_3368_length_18610_cov_7.372363 Viral contig found in MAG ERR7745867_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 62.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586263 sample name Hadza_MoBio_hadza-I-L_K_21_2489__NODE_3368_length_18610_cov_7.372363 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.5235 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142305 SAMEA13540339 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7745867. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540339 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 10.7247 MAG coverage software Reads (ERR7745867) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559896) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-I-L_K_21_2489__NODE_654_length_65458_cov_6.163411 Viral contig found in MAG ERR7745867_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586263 sample name Hadza_MoBio_hadza-I-L_K_21_2489__NODE_654_length_65458_cov_6.163411 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.599 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11142306 SAMEA13540340 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745870. BACPHLIP temperate score 0.0254285490843079 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540340 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 9.93921 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 113 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1293_length_49140_cov_5.384526_1 Viral contig found in MAG ERR7745870_bin.304 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1293_length_49140_cov_5.384526_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_provirus.1293 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142307 SAMEA13540341 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745870. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540341 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 17.0139 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 223 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_2307_length_33131_cov_9.638682_1 Viral contig found in MAG ERR7745870_bin.7 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_2307_length_33131_cov_9.638682_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127;s__CAG-127 sp900319515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_provirus.2307 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142308 SAMEA13540342 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745870. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540342 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 21.3306 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1154 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_51_length_241661_cov_12.071420_1 Viral contig found in MAG ERR7745870_bin.12 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_51_length_241661_cov_12.071420_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME067489 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-217;s__CAG-217 sp000436335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_provirus.51 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142309 SAMEA13540343 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745870. BACPHLIP temperate score 0.00994313231849539 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540343 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 11.2197 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_829_length_63667_cov_6.533260_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_829_length_63667_cov_6.533260_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900542795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.115 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142310 SAMEA13540344 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7745870. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540344 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 301.341 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1164_length_52246_cov_175.800782 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1164_length_52246_cov_175.800782 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.470 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11142311 SAMEA13540345 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745870. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540345 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 25.9203 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1469_length_45091_cov_14.390945 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1469_length_45091_cov_14.390945 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_virus.1469 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142312 SAMEA13540346 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745870. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540346 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 671.847 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 343 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1624_length_42273_cov_364.127642 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1624_length_42273_cov_364.127642 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_virus.1624 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142313 SAMEA13540347 1701671 uncultured podovirus This sample represents an uncultured Vibrio phage 1.205.O._10N.222.51.A7 virus assembled from ERR7745870. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540347 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 90.0827 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 82 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1782_length_39531_cov_53.541517 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1782_length_39531_cov_53.541517 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.1416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Vibrio phage 1.205.O._10N.222.51.A7 virus enrichment approach none ERS11142314 SAMEA13540348 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745870. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540348 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 155.862 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1916_length_37738_cov_91.881894 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_1916_length_37738_cov_91.881894 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745420_virus.171 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142315 SAMEA13540349 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745870. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540349 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 54.0905 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_2081_length_35583_cov_32.233059 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_2081_length_35583_cov_32.233059 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738144_virus.294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142316 SAMEA13540350 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7745870. BACPHLIP temperate score 0.15387564972157636 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540350 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 8.38836 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 189 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_2770_length_28920_cov_4.772319 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_2770_length_28920_cov_4.772319 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.2014 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11142317 SAMEA13540351 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745870. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540351 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 15.5313 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_3611_length_23812_cov_8.302549 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_3611_length_23812_cov_8.302549 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_virus.3611 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142318 SAMEA13540352 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745870. BACPHLIP temperate score 0.01358752575482346 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540352 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 11.5619 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_4565_length_20087_cov_6.677261 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_4565_length_20087_cov_6.677261 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738567_virus.16 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142319 SAMEA13540353 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745870. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540353 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 95.8647 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_642_length_73291_cov_52.882960 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_642_length_73291_cov_52.882960 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_virus.642 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142320 SAMEA13540354 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745870. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540354 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 11.1147 MAG coverage software Reads (ERR7745870) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560649) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 1264 Submitter Id Hadza_MoBio_hadza-E-H_A_15_1703__NODE_921_length_59973_cov_6.490400 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6829268292682927 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585946 sample name Hadza_MoBio_hadza-E-H_A_15_1703__NODE_921_length_59973_cov_6.490400 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142321 SAMEA13540355 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745874. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540355 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 61.1919 MAG coverage software Reads (ERR7745874) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566850) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 54 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_MoBio_hadza-A-D_J_13_1546__NODE_47_length_115207_cov_36.976027_1 Viral contig found in MAG ERR7745874_bin.49 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585800 sample name Hadza_MoBio_hadza-A-D_J_13_1546__NODE_47_length_115207_cov_36.976027_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142322 SAMEA13540356 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745874. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540356 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 55.1281 MAG coverage software Reads (ERR7745874) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566850) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 82 Submitter Id Hadza_MoBio_hadza-A-D_J_13_1546__NODE_174_length_72699_cov_33.726570 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585800 sample name Hadza_MoBio_hadza-A-D_J_13_1546__NODE_174_length_72699_cov_33.726570 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745874_virus.174 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142323 SAMEA13540357 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745874. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540357 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 7.32458 MAG coverage software Reads (ERR7745874) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566850) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_J_13_1546__NODE_447_length_44444_cov_4.380598 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585800 sample name Hadza_MoBio_hadza-A-D_J_13_1546__NODE_447_length_44444_cov_4.380598 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745414_bin.186 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900768625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738447_virus.891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142324 SAMEA13540358 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745874. BACPHLIP temperate score 0.15726046508259311 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540358 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 131.664 MAG coverage software Reads (ERR7745874) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566850) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-A-D_J_13_1546__NODE_914_length_28452_cov_78.867736 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585800 sample name Hadza_MoBio_hadza-A-D_J_13_1546__NODE_914_length_28452_cov_78.867736 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738199_virus.353 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142325 SAMEA13540359 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745876. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540359 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 989.588 MAG coverage software Reads (ERR7745876) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560456) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_K_22_1919__NODE_94_length_94246_cov_567.890038_1 Viral contig found in MAG ERR7745876_bin.14 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586062 sample name Hadza_MoBio_hadza-E-H_K_22_1919__NODE_94_length_94246_cov_567.890038_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745876_provirus.94 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142326 SAMEA13540360 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745876. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540360 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 1517.24 MAG coverage software Reads (ERR7745876) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560456) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 500 Submitter Id Hadza_MoBio_hadza-E-H_K_22_1919__NODE_40_length_152796_cov_876.808033 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.48 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586062 sample name Hadza_MoBio_hadza-E-H_K_22_1919__NODE_40_length_152796_cov_876.808033 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides distasonis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745876_virus.40 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142327 SAMEA13540361 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745877. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540361 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 23.6248 MAG coverage software Reads (ERR7745877) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567266) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 62 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_135_length_107070_cov_14.077697_1 Viral contig found in MAG ERR7745877_bin.36 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787383 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_135_length_107070_cov_14.077697_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1650 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142328 SAMEA13540362 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll provirus assembled from ERR7745877. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540362 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 57.0044 MAG coverage software Reads (ERR7745877) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567266) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 121 Number of CRISPR spacer hits supporting host taxonomy 89 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_9_length_349608_cov_34.055506_1 Viral contig found in MAG ERR7745877_bin.79 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787383 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_9_length_349608_cov_34.055506_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745877_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11142329 SAMEA13540363 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade sp. virus assembled from ERR7745877. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540363 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 293.331 MAG coverage software Reads (ERR7745877) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567266) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_144_length_104763_cov_174.908603 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6692913385826772 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787383 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_144_length_104763_cov_174.908603 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738572_virus.342 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; UAG-readthrough crAss clade sp. virus enrichment approach none ERS11142330 SAMEA13540364 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7745877. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540364 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 68.6622 MAG coverage software Reads (ERR7745877) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567266) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 54 Number of CRISPR spacer hits supporting host taxonomy 413 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_538_length_54560_cov_41.261972 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787383 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_538_length_54560_cov_41.261972 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738574_virus.239 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11142331 SAMEA13540365 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7745877. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540365 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 110.853 MAG coverage software Reads (ERR7745877) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567266) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 387 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_709_length_45996_cov_68.345108 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4090909090909091 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787383 sample name Nepal_MoBio_Fiber-Hadza-Nepal_J_3_RAU0015YZ__NODE_709_length_45996_cov_68.345108 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745877_virus.709 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11142332 SAMEA13540366 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745881. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540366 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 35.0323 MAG coverage software Reads (ERR7745881) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_C-REDO_A_5_1505__NODE_104_length_150221_cov_20.304155_1 Viral contig found in MAG ERR7745881_bin.19 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585761 sample name Hadza_MoBio_C-REDO_A_5_1505__NODE_104_length_150221_cov_20.304155_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-460;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745408_provirus.49 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142333 SAMEA13540367 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745881. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540367 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 20.08 MAG coverage software Reads (ERR7745881) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 72 Number of CRISPR spacer hits supporting host taxonomy 282 Submitter Id Hadza_MoBio_C-REDO_A_5_1505__NODE_391_length_78502_cov_11.360179_1 Viral contig found in MAG ERR7745881_bin.29 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585761 sample name Hadza_MoBio_C-REDO_A_5_1505__NODE_391_length_78502_cov_11.360179_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372998 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142334 SAMEA13540368 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745881. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540368 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 143.996 MAG coverage software Reads (ERR7745881) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_C-REDO_A_5_1505__NODE_1022_length_41010_cov_81.693401 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585761 sample name Hadza_MoBio_C-REDO_A_5_1505__NODE_1022_length_41010_cov_81.693401 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.551 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142335 SAMEA13540369 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745881. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540369 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 15.9018 MAG coverage software Reads (ERR7745881) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 77 Submitter Id Hadza_MoBio_C-REDO_A_5_1505__NODE_1506_length_30840_cov_8.902448 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585761 sample name Hadza_MoBio_C-REDO_A_5_1505__NODE_1506_length_30840_cov_8.902448 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-451;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745914_virus.1335 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142336 SAMEA13540370 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745881. BACPHLIP temperate score 0.03912499170499385 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540370 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 57.5208 MAG coverage software Reads (ERR7745881) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_C-REDO_A_5_1505__NODE_2318_length_22508_cov_32.990058 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585761 sample name Hadza_MoBio_C-REDO_A_5_1505__NODE_2318_length_22508_cov_32.990058 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_provirus.40 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142337 SAMEA13540371 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745881. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540371 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 106.054 MAG coverage software Reads (ERR7745881) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_C-REDO_A_5_1505__NODE_550_length_63491_cov_60.197748 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585761 sample name Hadza_MoBio_C-REDO_A_5_1505__NODE_550_length_63491_cov_60.197748 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME192801 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp000432135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745881_virus.550 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142338 SAMEA13540372 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745881. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540372 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 12.4252 MAG coverage software Reads (ERR7745881) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561357) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_C-REDO_A_5_1505__NODE_928_length_44410_cov_6.973699 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585761 sample name Hadza_MoBio_C-REDO_A_5_1505__NODE_928_length_44410_cov_6.973699 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.328 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__UBA1750;g__UBA7102;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3320 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142339 SAMEA13540373 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus provirus assembled from ERR7745884. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540373 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 49.4824 MAG coverage software Reads (ERR7745884) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567335) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_21_THA0055JZ__NODE_437_length_52778_cov_28.398854_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9310344827586208 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787394 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_21_THA0055JZ__NODE_437_length_52778_cov_28.398854_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745884_provirus.437 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11142340 SAMEA13540374 2133760 Siphoviridae environmental samples This sample represents an uncultured unclassified Dhillonvirus virus assembled from ERR7745884. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540374 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 1086.94 MAG coverage software Reads (ERR7745884) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567335) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_21_THA0055JZ__NODE_538_length_44618_cov_616.822860 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7903225806451613 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787394 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_21_THA0055JZ__NODE_538_length_44618_cov_616.822860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745884_virus.538 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Dhillonvirus; unclassified Dhillonvirus virus enrichment approach none ERS11142341 SAMEA13540375 1701671 uncultured podovirus This sample represents an uncultured Lederbergvirus virus assembled from ERR7745884. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540375 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 210.122 MAG coverage software Reads (ERR7745884) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567335) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2551 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_F_21_THA0055JZ__NODE_931_length_26947_cov_119.269483 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.392156862745098 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787394 sample name Nepal_MoBio_Fiber-Hadza-Nepal_F_21_THA0055JZ__NODE_931_length_26947_cov_119.269483 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745884_virus.931 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Lederbergvirus virus enrichment approach none ERS11142342 SAMEA13540376 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745888. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540376 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 21.269 MAG coverage software Reads (ERR7745888) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560445) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_E_4_1847__NODE_425_length_38365_cov_12.798710_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8529411764705882 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586032 sample name Hadza_MoBio_hadza-E-H_E_4_1847__NODE_425_length_38365_cov_12.798710_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745888_provirus.425 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142343 SAMEA13540377 2133760 Siphoviridae environmental samples This sample represents an uncultured Phietavirus virus assembled from ERR7745888. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540377 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 93.9404 MAG coverage software Reads (ERR7745888) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560445) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_E_4_1847__NODE_370_length_41638_cov_55.629653 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; HMM-based (lower-bound) completeness score 54.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586032 sample name Hadza_MoBio_hadza-E-H_E_4_1847__NODE_370_length_41638_cov_55.629653 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107646 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella;s__Weissella confusa vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745888_virus.370 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Azeredovirinae; Phietavirus virus enrichment approach none ERS11142344 SAMEA13540378 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745888. BACPHLIP temperate score 0.12890747351253778 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540378 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 86.9211 MAG coverage software Reads (ERR7745888) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560445) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_E_4_1847__NODE_675_length_26638_cov_63.420654 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-11 completeness approach CheckV; AAI-based (medium-confidence) completeness score 69.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586032 sample name Hadza_MoBio_hadza-E-H_E_4_1847__NODE_675_length_26638_cov_63.420654 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107646 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella;s__Weissella confusa vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745888_virus.675 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142345 SAMEA13540379 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745890. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540379 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 182.9 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1227_length_61302_cov_107.211482_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1227_length_61302_cov_107.211482_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142346 SAMEA13540380 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745890. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540380 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 70.4447 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1996_length_45589_cov_42.393523_1 Viral contig found in MAG ERR7745890_bin.29 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1996_length_45589_cov_42.393523_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1049 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142347 SAMEA13540381 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7745890. BACPHLIP temperate score 0.08997797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540381 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 28.9624 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 127 Number of CRISPR spacer hits supporting host taxonomy 97 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_275_length_131465_cov_17.003455_1 Viral contig found in MAG ERR7745890_bin.403 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_275_length_131465_cov_17.003455_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_provirus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11142348 SAMEA13540382 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745890. BACPHLIP temperate score 0.16238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540382 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 177.675 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 199 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_5_length_464791_cov_104.454279_1_1 Viral contig found in MAG ERR7745890_bin.267 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_5_length_464791_cov_104.454279_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.3188 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142349 SAMEA13540383 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745890. BACPHLIP temperate score 0.3636550413062912 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540383 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 20.5151 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 75 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_90_length_215247_cov_17.340554_1 Viral contig found in MAG ERR7745890_bin.241 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_90_length_215247_cov_17.340554_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000967 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum;s__Anaerotignum faecicola vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.90 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142350 SAMEA13540384 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745890. BACPHLIP temperate score 0.12578965839962564 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540384 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 18.2347 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1143_length_63883_cov_10.213632 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1143_length_63883_cov_10.213632 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.1218 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142351 SAMEA13540385 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745890. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540385 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 17.8851 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 200 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1618_length_51783_cov_11.547963 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_1618_length_51783_cov_11.547963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738617_virus.261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142352 SAMEA13540386 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745890. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540386 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 23.0769 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 656 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_2163_length_43191_cov_13.764230 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_2163_length_43191_cov_13.764230 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0331678 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142353 SAMEA13540387 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745890. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540387 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 12.9231 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 347 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_2411_length_39730_cov_7.206743 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_2411_length_39730_cov_7.206743 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738537_virus.2114 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142354 SAMEA13540388 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745890. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540388 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 41.2143 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 72 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_2652_length_37369_cov_24.613349 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_2652_length_37369_cov_24.613349 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738144_virus.294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142355 SAMEA13540389 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745890. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540389 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 45.8575 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 810 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_3112_length_33193_cov_30.983814 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_3112_length_33193_cov_30.983814 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0316936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142356 SAMEA13540390 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745890. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540390 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 22.2976 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 200 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_3815_length_28612_cov_13.329876 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_3815_length_28612_cov_13.329876 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000448 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900066885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.3815 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142357 SAMEA13540391 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745890. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540391 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 29.8414 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_435_length_107547_cov_17.097562 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_435_length_107547_cov_17.097562 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738537_virus.190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142358 SAMEA13540392 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7745890. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540392 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 80.6454 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_498_length_100390_cov_45.052685 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.990990990990991 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_498_length_100390_cov_45.052685 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.346 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11142359 SAMEA13540393 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745890. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540393 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:41Z INSDC last update 2022-12-27T01:22:41Z INSDC status public MAG coverage depth 58.663 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 242 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_604_length_90934_cov_34.167164 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.30434782608695654 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_604_length_90934_cov_34.167164 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.604 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142360 SAMEA13540394 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7745890. BACPHLIP temperate score 0.06574293217546884 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540394 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 32.2191 MAG coverage software Reads (ERR7745890) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560264) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_F_18_2239__NODE_7150_length_17442_cov_18.574201 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586162 sample name Hadza_MoBio_hadza-E-H_F_18_2239__NODE_7150_length_17442_cov_18.574201 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME027723 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A;s__Coprococcus_A catus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.5217 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11142361 SAMEA13540395 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745896. BACPHLIP temperate score 0.3203913925708577 ENA-FIRST-PUBLIC 2022-12-27T01:22:40Z ENA-LAST-UPDATE 2022-12-27T01:22:40Z External Id SAMEA13540395 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 66.7501 MAG coverage software Reads (ERR7745896) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562242) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_F_14_1634__NODE_133_length_81856_cov_38.553920_1 Viral contig found in MAG ERR7745896_bin.61 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585878 sample name Hadza_MoBio_hadza-A-D_F_14_1634__NODE_133_length_81856_cov_38.553920_1 scientific_name Siphoviridae environmental samples sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME138453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus;s__Lactococcus lactis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745896_provirus.133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae ERS11142362 SAMEA13540396 1701671 uncultured podovirus This sample represents an uncultured Lederbergvirus virus assembled from ERR7745896. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540396 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 123.613 MAG coverage software Reads (ERR7745896) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562242) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1281 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_F_14_1634__NODE_1103_length_21783_cov_70.250530 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585878 sample name Hadza_MoBio_hadza-A-D_F_14_1634__NODE_1103_length_21783_cov_70.250530 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745896_virus.1103 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Lederbergvirus virus enrichment approach none ERS11142363 SAMEA13540397 2133760 Siphoviridae environmental samples This sample represents an uncultured Actinomyces phage xhp1 virus assembled from ERR7745896. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540397 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 9.54622 MAG coverage software Reads (ERR7745896) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562242) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_F_14_1634__NODE_508_length_34801_cov_5.350190 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585878 sample name Hadza_MoBio_hadza-A-D_F_14_1634__NODE_508_length_34801_cov_5.350190 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME207226 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia;s__Pauljensenia sp001838165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745896_virus.508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Actinomyces phage xhp1 virus enrichment approach none ERS11142364 SAMEA13540398 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745897. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540398 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 14.4886 MAG coverage software Reads (ERR7745897) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561483) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_N_21_1514__NODE_180_length_88101_cov_8.423373_1 Viral contig found in MAG ERR7745897_bin.64 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585770 sample name Hadza_MoBio_hadza-A-D_N_21_1514__NODE_180_length_88101_cov_8.423373_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738233_virus.443 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142365 SAMEA13540399 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745897. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540399 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 44.4333 MAG coverage software Reads (ERR7745897) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561483) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 752 Submitter Id Hadza_MoBio_hadza-A-D_N_21_1514__NODE_604_length_46195_cov_27.040483_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585770 sample name Hadza_MoBio_hadza-A-D_N_21_1514__NODE_604_length_46195_cov_27.040483_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738254_virus.235 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142366 SAMEA13540400 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745897. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540400 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 8.6122 MAG coverage software Reads (ERR7745897) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561483) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 107 Submitter Id Hadza_MoBio_hadza-A-D_N_21_1514__NODE_1180_length_30196_cov_4.998838 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585770 sample name Hadza_MoBio_hadza-A-D_N_21_1514__NODE_1180_length_30196_cov_4.998838 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1989 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142367 SAMEA13540401 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7745897. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540401 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 34.9069 MAG coverage software Reads (ERR7745897) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561483) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_N_21_1514__NODE_3772_length_12784_cov_43.576926 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585770 sample name Hadza_MoBio_hadza-A-D_N_21_1514__NODE_3772_length_12784_cov_43.576926 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128517 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900290275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745565_virus.3795 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11142368 SAMEA13540402 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745897. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540402 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 58.261 MAG coverage software Reads (ERR7745897) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561483) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 100 Submitter Id Hadza_MoBio_hadza-A-D_N_21_1514__NODE_689_length_42654_cov_34.081100 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585770 sample name Hadza_MoBio_hadza-A-D_N_21_1514__NODE_689_length_42654_cov_34.081100 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142369 SAMEA13540403 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745903. BACPHLIP temperate score 0.18718388309858397 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540403 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 9.87625 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 188 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_1142_length_43503_cov_6.055405_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_1142_length_43503_cov_6.055405_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.224 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__Ruminococcus sp900540005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_provirus.298 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142370 SAMEA13540404 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7745903. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540404 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 16.1436 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 213 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_231_length_99659_cov_9.788486_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8787878787878788 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_231_length_99659_cov_9.788486_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_C vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_provirus.687 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11142371 SAMEA13540405 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745903. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540405 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 11.2547 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_531_length_67730_cov_6.868047_1 Viral contig found in MAG ERR7745903_bin.166 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_531_length_67730_cov_6.868047_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.999 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142372 SAMEA13540406 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus virus assembled from ERR7745903. BACPHLIP temperate score 0.9019553881807648 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540406 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 23.6783 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 476 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_1035_length_45898_cov_14.457585 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_1035_length_45898_cov_14.457585 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_virus.1035 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11142373 SAMEA13540407 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745903. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540407 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 16.2376 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 130 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_1381_length_38567_cov_9.877579 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.68 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_1381_length_38567_cov_9.877579 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142374 SAMEA13540408 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745903. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540408 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 110.955 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 591 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_199_length_106835_cov_67.858587 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.96 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_199_length_106835_cov_67.858587 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142375 SAMEA13540409 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745903. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540409 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 10.4837 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_330_length_85399_cov_6.351551 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9387755102040816 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_330_length_85399_cov_6.351551 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_virus.330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142376 SAMEA13540410 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745903. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540410 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 11.568 MAG coverage software Reads (ERR7745903) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561239) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_F_4_1629__NODE_8215_length_9320_cov_7.071189 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-02-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585873 sample name Hadza_MoBio_hadza-A-D_F_4_1629__NODE_8215_length_9320_cov_7.071189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME089567 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp001556435 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_virus.8215 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142377 SAMEA13540411 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745906. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540411 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 26.0977 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 312 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1546_length_36422_cov_17.162828_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1546_length_36422_cov_17.162828_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_provirus.1546 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142378 SAMEA13540412 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745906. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540412 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 26.87 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_392_length_83590_cov_16.216182_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_392_length_83590_cov_16.216182_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_provirus.392 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142379 SAMEA13540413 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745906. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540413 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 29.2264 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_794_length_55217_cov_16.691567_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_794_length_55217_cov_16.691567_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.329 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__UBA1191 sp900549125 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_provirus.794 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142380 SAMEA13540414 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745906. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540414 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 33.4611 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1056_length_45871_cov_18.943202 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1056_length_45871_cov_18.943202 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.1056 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142381 SAMEA13540415 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745906. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540415 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 14.6541 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 121 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1237_length_41886_cov_8.388744 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1237_length_41886_cov_8.388744 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.1237 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142382 SAMEA13540416 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745906. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540416 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 35.1277 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 596 Number of CRISPR spacer hits supporting host taxonomy 282 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1349_length_39543_cov_21.888917 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1349_length_39543_cov_21.888917 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.1349 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142383 SAMEA13540417 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745906. BACPHLIP temperate score 0.2875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540417 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 18.197 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1608_length_35585_cov_10.239129 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_1608_length_35585_cov_10.239129 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.1608 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142384 SAMEA13540418 340016 uncultured virus This sample represents an uncultured Inovirus sp. virus assembled from ERR7745906. BACPHLIP temperate score 0.0024238520115018 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540418 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 14.6254 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 112 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_23489_length_5033_cov_8.836965 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_23489_length_5033_cov_8.836965 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.23489 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Loebvirae; Hofneiviricota; Faserviricetes; Tubulavirales; Inoviridae; Inovirus; unclassified Inovirus; Inovirus sp. virus enrichment approach none ERS11142385 SAMEA13540419 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745906. BACPHLIP temperate score 0.08920704845814986 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540419 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 8.45944 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_2853_length_24841_cov_4.749919 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_2853_length_24841_cov_4.749919 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_provirus.277 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142386 SAMEA13540420 2133760 Siphoviridae environmental samples This sample represents an uncultured Streptococcus phage Javan351 virus assembled from ERR7745906. BACPHLIP temperate score 0.00270137614315428 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540420 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 12.1278 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_3749_length_20437_cov_6.949558 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_3749_length_20437_cov_6.949558 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME086861 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter;s__Fusicatenibacter saccharivorans vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.3749 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Streptococcus phage Javan351 virus enrichment approach none ERS11142387 SAMEA13540421 2100421 uncultured Caudovirales phage This sample represents an uncultured Gregsiragusavirus virus assembled from ERR7745906. BACPHLIP temperate score 0.18368843659633977 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540421 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 10.0234 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_5002_length_16623_cov_5.752146 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_5002_length_16623_cov_5.752146 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.5002 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Guelinviridae; Denniswatsonvirinae; Gregsiragusavirus virus enrichment approach none ERS11142388 SAMEA13540422 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745906. BACPHLIP temperate score 0.05680120315873836 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540422 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 23.2462 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_684_length_60622_cov_13.300074 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.945945945945946 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_684_length_60622_cov_13.300074 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.684 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142389 SAMEA13540423 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745906. BACPHLIP temperate score 0.10836869769395652 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540423 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 12.2082 MAG coverage software Reads (ERR7745906) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560435) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_A_12_1819__NODE_928_length_50295_cov_7.206759 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-29 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586019 sample name Hadza_MoBio_hadza-E-H_A_12_1819__NODE_928_length_50295_cov_7.206759 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME116282 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873;s__CAG-873 sp001701165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.928 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142390 SAMEA13540424 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745908. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540424 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 21.0345 MAG coverage software Reads (ERR7745908) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567563) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 525 Number of CRISPR spacer hits supporting host taxonomy 332 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1472_length_41277_cov_11.626214_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787411 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1472_length_41277_cov_11.626214_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0278621 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142391 SAMEA13540425 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745908. BACPHLIP temperate score 0.15446967015660706 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540425 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 67.9763 MAG coverage software Reads (ERR7745908) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567563) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_608_length_80713_cov_38.919019_1 Viral contig found in MAG ERR7745908_bin.8 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787411 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_608_length_80713_cov_38.919019_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME181333 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900540885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0314975 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142392 SAMEA13540426 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745908. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540426 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 14.2116 MAG coverage software Reads (ERR7745908) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567563) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 125 Number of CRISPR spacer hits supporting host taxonomy 1966 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1183_length_49421_cov_7.937155 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6388888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787411 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1183_length_49421_cov_7.937155 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745346_virus.2531 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142393 SAMEA13540427 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745908. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540427 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 9.74324 MAG coverage software Reads (ERR7745908) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567563) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1546_length_39452_cov_5.355124 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787411 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1546_length_39452_cov_5.355124 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738560_virus.593 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142394 SAMEA13540428 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745908. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540428 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 13.3284 MAG coverage software Reads (ERR7745908) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567563) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1906_length_32011_cov_7.474698 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7083333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787411 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_1906_length_32011_cov_7.474698 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745908_virus.1906 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142395 SAMEA13540429 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745908. BACPHLIP temperate score 0.16462237831743523 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540429 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 11.3941 MAG coverage software Reads (ERR7745908) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567563) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 452 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_2674_length_22816_cov_6.273187 Viral contig found in MAG ERR7745908_bin.153 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787411 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_2674_length_22816_cov_6.273187 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000511 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides fragilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738272_provirus.4 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142396 SAMEA13540430 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745908. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540430 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 61.9508 MAG coverage software Reads (ERR7745908) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567563) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_609_length_80647_cov_34.519995 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6382978723404256 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787411 sample name Nepal_MoBio_Fiber-Hadza-Nepal_D_5_THA1074JZ__NODE_609_length_80647_cov_34.519995 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745908_virus.609 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142397 SAMEA13540431 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745914. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540431 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 17.3422 MAG coverage software Reads (ERR7745914) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560967) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_C-REDO_E_2_1553__NODE_11_length_330723_cov_9.929196_1 Viral contig found in MAG ERR7745914_bin.68 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585807 sample name Hadza_MoBio_C-REDO_E_2_1553__NODE_11_length_330723_cov_9.929196_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME039567 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632;s__CAG-632 sp900539185 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_provirus.34 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142398 SAMEA13540432 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745914. BACPHLIP temperate score 0.8769553881807648 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540432 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 45.5096 MAG coverage software Reads (ERR7745914) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560967) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_C-REDO_E_2_1553__NODE_1023_length_37423_cov_26.879532 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585807 sample name Hadza_MoBio_C-REDO_E_2_1553__NODE_1023_length_37423_cov_26.879532 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745914_virus.1023 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142399 SAMEA13540433 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745914. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540433 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 8.58515 MAG coverage software Reads (ERR7745914) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560967) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 183 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_C-REDO_E_2_1553__NODE_1569_length_27254_cov_4.849836 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585807 sample name Hadza_MoBio_C-REDO_E_2_1553__NODE_1569_length_27254_cov_4.849836 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0261276 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142400 SAMEA13540434 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745914. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540434 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 16.8035 MAG coverage software Reads (ERR7745914) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560967) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 77 Submitter Id Hadza_MoBio_C-REDO_E_2_1553__NODE_2506_length_19225_cov_9.667276 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585807 sample name Hadza_MoBio_C-REDO_E_2_1553__NODE_2506_length_19225_cov_9.667276 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_virus.395 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142401 SAMEA13540435 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745914. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540435 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 482.676 MAG coverage software Reads (ERR7745914) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560967) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_C-REDO_E_2_1553__NODE_719_length_46995_cov_283.022742 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585807 sample name Hadza_MoBio_C-REDO_E_2_1553__NODE_719_length_46995_cov_283.022742 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.262 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3024 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142402 SAMEA13540436 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745914. BACPHLIP temperate score 0.12747797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540436 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 18.2388 MAG coverage software Reads (ERR7745914) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560967) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_E_2_1553__NODE_843_length_42231_cov_10.754733 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585807 sample name Hadza_MoBio_C-REDO_E_2_1553__NODE_843_length_42231_cov_10.754733 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142403 SAMEA13540437 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745918. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540437 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 36.7462 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1103_length_51690_cov_21.516033_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1103_length_51690_cov_21.516033_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.242 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142404 SAMEA13540438 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745918. BACPHLIP temperate score 0.02549472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540438 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 21.3087 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 106 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_321_length_104582_cov_12.479250_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_321_length_104582_cov_12.479250_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.160 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142405 SAMEA13540439 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7745918. BACPHLIP temperate score 0.26745594713656384 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540439 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 71.1628 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_613_length_73985_cov_42.771770_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9393939393939394 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_613_length_73985_cov_42.771770_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738234_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_provirus.613 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142406 SAMEA13540440 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745918. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540440 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 76.089 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 614 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1094_length_52052_cov_44.043098 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1094_length_52052_cov_44.043098 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142407 SAMEA13540441 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745918. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540441 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 128.423 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1453_length_42858_cov_71.654333 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4166666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1453_length_42858_cov_71.654333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME020571 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp002404795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.1453 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142408 SAMEA13540442 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745918. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540442 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 13.8664 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1653_length_39374_cov_7.810622 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1653_length_39374_cov_7.810622 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738271_virus.1435 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142409 SAMEA13540443 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745918. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540443 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 19.5106 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1768_length_37780_cov_11.405034 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_1768_length_37780_cov_11.405034 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.1126 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142410 SAMEA13540444 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745918. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540444 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 41.4247 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_2026_length_34058_cov_25.067773 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_2026_length_34058_cov_25.067773 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.1992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142411 SAMEA13540445 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745918. BACPHLIP temperate score 0.3616465191540744 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540445 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 49.9974 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_2723_length_27120_cov_28.300189 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_2723_length_27120_cov_28.300189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738227_bin.197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp004557855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.2723 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142412 SAMEA13540446 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745918. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540446 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 13.8835 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 102 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_3768_length_20594_cov_8.127602 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_3768_length_20594_cov_8.127602 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.3768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142413 SAMEA13540447 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745918. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540447 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 45.5628 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_679_length_69852_cov_28.313579 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8636363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_679_length_69852_cov_28.313579 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745918_virus.679 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142414 SAMEA13540448 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745918. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540448 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 160.166 MAG coverage software Reads (ERR7745918) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561744) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 369 Number of CRISPR spacer hits supporting host taxonomy 144 Submitter Id Hadza_MoBio_hadza-I-L_J_9_1249__NODE_970_length_56550_cov_94.704372 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585667 sample name Hadza_MoBio_hadza-I-L_J_9_1249__NODE_970_length_56550_cov_94.704372 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000434975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.1267 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142415 SAMEA13540449 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745919. BACPHLIP temperate score 0.04234581497797356 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540449 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 23.8203 MAG coverage software Reads (ERR7745919) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_C-REDO_D_7_1547__NODE_396_length_77562_cov_13.382164_1 Viral contig found in MAG ERR7745919_bin.204 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585801 sample name Hadza_MoBio_C-REDO_D_7_1547__NODE_396_length_77562_cov_13.382164_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.2010 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142416 SAMEA13540450 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745919. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540450 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 11.9955 MAG coverage software Reads (ERR7745919) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_C-REDO_D_7_1547__NODE_1051_length_37158_cov_6.775276 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585801 sample name Hadza_MoBio_C-REDO_D_7_1547__NODE_1051_length_37158_cov_6.775276 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME192801 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp000432135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.1634 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142417 SAMEA13540451 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745919. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540451 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 27.093 MAG coverage software Reads (ERR7745919) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_C-REDO_D_7_1547__NODE_1662_length_26215_cov_17.884919 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585801 sample name Hadza_MoBio_C-REDO_D_7_1547__NODE_1662_length_26215_cov_17.884919 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_virus.1662 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142418 SAMEA13540452 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745919. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540452 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 10.5526 MAG coverage software Reads (ERR7745919) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 171 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_C-REDO_D_7_1547__NODE_2444_length_19191_cov_5.859527 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585801 sample name Hadza_MoBio_C-REDO_D_7_1547__NODE_2444_length_19191_cov_5.859527 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.79 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;s__Ruminiclostridium_E siraeum vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_virus.2095 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142419 SAMEA13540453 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745919. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540453 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 21.471 MAG coverage software Reads (ERR7745919) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_C-REDO_D_7_1547__NODE_509_length_65292_cov_12.157954 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; HMM-based (lower-bound) completeness score 81.31 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585801 sample name Hadza_MoBio_C-REDO_D_7_1547__NODE_509_length_65292_cov_12.157954 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738611_provirus.784 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142420 SAMEA13540454 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745919. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540454 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 73.5435 MAG coverage software Reads (ERR7745919) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_C-REDO_D_7_1547__NODE_784_length_47510_cov_42.172369 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585801 sample name Hadza_MoBio_C-REDO_D_7_1547__NODE_784_length_47510_cov_42.172369 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746349_bin.268 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA5920;s__UBA5920 sp002406055 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_virus.784 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142421 SAMEA13540455 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745919. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540455 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 25.0198 MAG coverage software Reads (ERR7745919) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560944) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 309 Submitter Id Hadza_MoBio_C-REDO_D_7_1547__NODE_956_length_40534_cov_14.496181 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585801 sample name Hadza_MoBio_C-REDO_D_7_1547__NODE_956_length_40534_cov_14.496181 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_virus.1795 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142422 SAMEA13540456 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745922. BACPHLIP temperate score 0.07305889139359004 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540456 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 9.12906 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_1937_length_30019_cov_5.355554_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_1937_length_30019_cov_5.355554_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747782_bin.13 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola sp000434735 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738160_provirus.796 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142423 SAMEA13540457 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745922. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540457 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 27.1078 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 105 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_559_length_64390_cov_16.921151_1 Viral contig found in MAG ERR7745922_bin.126 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_559_length_64390_cov_16.921151_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.945 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142424 SAMEA13540458 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745922. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540458 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 8.91391 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 93 Number of CRISPR spacer hits supporting host taxonomy 489 Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_1549_length_34857_cov_5.196521 Viral contig found in MAG ERR7745922_bin.81 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_1549_length_34857_cov_5.196521 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746344_virus.2132 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142425 SAMEA13540459 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745922. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540459 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 140.708 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 252 Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_204_length_103845_cov_83.050362 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9117647058823528 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_204_length_103845_cov_83.050362 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737971_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900548745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745384_virus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142426 SAMEA13540460 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745922. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540460 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 11.9991 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 166 Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_2448_length_24907_cov_7.055658 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_2448_length_24907_cov_7.055658 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745922_virus.2448 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142427 SAMEA13540461 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7745922. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540461 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 24.5918 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_31_length_220447_cov_14.539298 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5535714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_31_length_220447_cov_14.539298 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11142428 SAMEA13540462 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745922. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540462 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 29.8662 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_5260_length_13011_cov_18.004661 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_5260_length_13011_cov_18.004661 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.262 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745384_virus.4192 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142429 SAMEA13540463 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745922. BACPHLIP temperate score 0.11194438650927264 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540463 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 25.5325 MAG coverage software Reads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 117 Submitter Id Hadza_MoBio_hadza-I-L_O_10_2644__NODE_986_length_46724_cov_15.441679 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586348 sample name Hadza_MoBio_hadza-I-L_O_10_2644__NODE_986_length_46724_cov_15.441679 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745389_virus.471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142430 SAMEA13540464 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745924. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540464 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 172.259 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_1206_length_70579_cov_99.421208_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_1206_length_70579_cov_99.421208_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125893 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger formicilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0250587 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142431 SAMEA13540465 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745924. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540465 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 308.21 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_1649_length_58097_cov_176.062634_1 Viral contig found in MAG ERR7745924_bin.268 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_1649_length_58097_cov_176.062634_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.1649 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142432 SAMEA13540466 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745924. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540466 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 18.6002 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_2264_length_47720_cov_10.626640_1 Viral contig found in MAG ERR7745924_bin.435 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_2264_length_47720_cov_10.626640_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738600_bin.112 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG14107;s__RUG14107 sp900772685 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_provirus.624 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142433 SAMEA13540467 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745924. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540467 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 16.0818 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_3189_length_37261_cov_9.113651_1 Viral contig found in MAG ERR7745924_bin.388 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4705882352941176 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_3189_length_37261_cov_9.113651_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.3189 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142434 SAMEA13540468 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745924. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540468 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:40Z INSDC last update 2022-12-27T01:22:40Z INSDC status public MAG coverage depth 37.2824 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 103 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_456_length_124164_cov_22.526622_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.3157894736842105 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_456_length_124164_cov_22.526622_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.456 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142435 SAMEA13540469 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745924. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540469 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 19.6624 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_784_length_90490_cov_11.682048_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9210526315789472 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_784_length_90490_cov_11.682048_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745924_bin.388 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.784 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142436 SAMEA13540470 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745924. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540470 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 13.896 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_92_length_242120_cov_8.312589_1 Viral contig found in MAG ERR7745924_bin.226 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8108108108108109 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_92_length_242120_cov_8.312589_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_provirus.1478 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142437 SAMEA13540471 1701671 uncultured podovirus This sample represents an uncultured Astrithrvirus virus assembled from ERR7745924. BACPHLIP temperate score 0.06876689984850125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540471 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 83.1471 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_13595_length_11466_cov_50.306419 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_13595_length_11466_cov_50.306419 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.9313 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus virus enrichment approach none ERS11142438 SAMEA13540472 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540472 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 52.1483 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_1805_length_55184_cov_29.984920 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 50.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_1805_length_55184_cov_29.984920 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.1805 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142439 SAMEA13540473 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540473 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 21.2632 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_2221_length_48324_cov_12.316413 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_2221_length_48324_cov_12.316413 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME255303 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales_A;f__UBA9506;g__UMGS755;s__UMGS755 sp900545185 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142440 SAMEA13540474 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.3093893088856105 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540474 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 10.0393 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_2727_length_41728_cov_5.546421 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_2727_length_41728_cov_5.546421 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.212 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia;s__Romboutsia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.2727 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142441 SAMEA13540475 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540475 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 9.58178 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 129 Number of CRISPR spacer hits supporting host taxonomy 298 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_3018_length_38895_cov_5.401051 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_3018_length_38895_cov_5.401051 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0319855 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142442 SAMEA13540476 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.09375054236578688 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540476 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 9.13485 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_3464_length_35064_cov_5.119273 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_3464_length_35064_cov_5.119273 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.3464 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142443 SAMEA13540477 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.13997797356828195 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540477 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 16.4328 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_4003_length_31391_cov_9.617392 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_4003_length_31391_cov_9.617392 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.1895 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142444 SAMEA13540478 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540478 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 19.4649 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_4390_length_29107_cov_11.158836 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8620689655172413 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_4390_length_29107_cov_11.158836 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.4390 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142445 SAMEA13540479 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540479 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 53.293 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_57_length_296491_cov_31.152968 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 15 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.49122807017543857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_57_length_296491_cov_31.152968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380120 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142446 SAMEA13540480 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745924. BACPHLIP temperate score 0.11938325991189436 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540480 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 27.0009 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 70 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_6600_length_21142_cov_16.957845 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_6600_length_21142_cov_16.957845 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024263 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides sp900549585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.6600 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142447 SAMEA13540481 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745924. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540481 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 28.304 MAG coverage software Reads (ERR7745924) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567885) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 411 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_754_length_92680_cov_16.627161 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_24_1660__NODE_754_length_92680_cov_16.627161 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.754 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142448 SAMEA13540482 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745937. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540482 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 9.0148 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_1045_length_37508_cov_5.436643_1 Viral contig found in MAG ERR7745937_bin.130 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_1045_length_37508_cov_5.436643_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745937_provirus.1045 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142449 SAMEA13540483 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745937. BACPHLIP temperate score 0.4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540483 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 32.3855 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_275_length_82133_cov_19.460637_1 Viral contig found in MAG ERR7745937_bin.29 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_275_length_82133_cov_19.460637_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_provirus.428 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142450 SAMEA13540484 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745937. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540484 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 44.8182 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_768_length_45993_cov_29.121287_1 Viral contig found in MAG ERR7745937_bin.7 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_768_length_45993_cov_29.121287_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME118160 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900552515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745937_provirus.768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142451 SAMEA13540485 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745937. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540485 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 11.7974 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_1255_length_33215_cov_6.913362 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_1255_length_33215_cov_6.913362 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745937_virus.1255 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142452 SAMEA13540486 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe virus assembled from ERR7745937. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540486 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 8.52297 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 350 Number of CRISPR spacer hits supporting host taxonomy 899 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_1533_length_29163_cov_4.966444 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48484848484848486 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_1533_length_29163_cov_4.966444 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0373039 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11142453 SAMEA13540487 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745937. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540487 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 13.7214 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 171 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_209_length_95368_cov_8.222728 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6296296296296297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_209_length_95368_cov_8.222728 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745937_virus.209 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142454 SAMEA13540488 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745937. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540488 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 20.6586 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_2687_length_19393_cov_12.324550 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_2687_length_19393_cov_12.324550 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738581_bin.271 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.3018 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142455 SAMEA13540489 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745937. BACPHLIP temperate score 0.0932089863334723 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540489 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 9.72347 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_411_length_66482_cov_5.624772 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_411_length_66482_cov_5.624772 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.161 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900545925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738180_virus.139 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142456 SAMEA13540490 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745937. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540490 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 12.6778 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 1173 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_539_length_57533_cov_7.599641 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; HMM-based (lower-bound) completeness score 64.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_539_length_57533_cov_7.599641 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA3388;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746233_virus.201 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142457 SAMEA13540491 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745937. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540491 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 35.8789 MAG coverage software Reads (ERR7745937) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561471) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 60 Submitter Id Hadza_MoBio_hadza-A-D_N_23_1513__NODE_849_length_42510_cov_21.474112 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; HMM-based (lower-bound) completeness score 62.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585769 sample name Hadza_MoBio_hadza-A-D_N_23_1513__NODE_849_length_42510_cov_21.474112 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745937_virus.849 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142458 SAMEA13540492 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745947. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540492 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 13.3922 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1203_length_67565_cov_7.502949_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1203_length_67565_cov_7.502949_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_provirus.1203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142459 SAMEA13540493 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7745947. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540493 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 28.3078 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 439 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_198_length_164666_cov_17.009253_1 Viral contig found in MAG ERR7745947_bin.234 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.951219512195122 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_198_length_164666_cov_17.009253_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142460 SAMEA13540494 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745947. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540494 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 15.5703 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_293_length_141518_cov_8.942061_1 Viral contig found in MAG ERR7745947_bin.204 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_293_length_141518_cov_8.942061_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_provirus.293 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142461 SAMEA13540495 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745947. BACPHLIP temperate score 0.09482695118618886 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540495 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 14.6202 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 104 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_772_length_88209_cov_8.410044_1 Viral contig found in MAG ERR7745947_bin.102 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 50.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_772_length_88209_cov_8.410044_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.1123 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142462 SAMEA13540496 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540496 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 11.3494 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 77 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1221_length_67010_cov_6.351635 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1221_length_67010_cov_6.351635 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.1221 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142463 SAMEA13540497 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540497 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 54.4905 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1411_length_61462_cov_31.008210 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8611111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1411_length_61462_cov_31.008210 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142464 SAMEA13540498 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540498 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 43.953 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1733_length_53856_cov_25.548467 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1733_length_53856_cov_25.548467 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7803603_bin.84 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.1733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142465 SAMEA13540499 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7745947. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540499 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 39.8743 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 97 Number of CRISPR spacer hits supporting host taxonomy 1038 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1950_length_49625_cov_23.113890 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5272727272727272 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_1950_length_49625_cov_23.113890 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0328330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11142466 SAMEA13540500 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745947. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540500 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 12.2952 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_21933_length_6562_cov_7.395220 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_21933_length_6562_cov_7.395220 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME272760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.17006 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142467 SAMEA13540501 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745947. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540501 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 45.3865 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 435 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2322_length_44386_cov_26.394705 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2322_length_44386_cov_26.394705 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.2030 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142468 SAMEA13540502 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 virus assembled from ERR7745947. BACPHLIP temperate score 0.4629947229551451 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540502 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 6120.73 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 169 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2518_length_42218_cov_3386.104744 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2518_length_42218_cov_3386.104744 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0280262 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11142469 SAMEA13540503 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540503 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 67.5134 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2698_length_40135_cov_40.210395 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2698_length_40135_cov_40.210395 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.1206 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142470 SAMEA13540504 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7745947. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540504 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 7.02296 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2835_length_38776_cov_3.799607 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_2835_length_38776_cov_3.799607 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018425 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__CAG-791 sp000431495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738565_virus.855 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11142471 SAMEA13540505 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540505 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 76.9507 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_3099_length_36009_cov_43.589669 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_3099_length_36009_cov_43.589669 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME116287 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281;s__UBA10281 sp900767815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.1534 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142472 SAMEA13540506 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540506 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 31.8801 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_330_length_136244_cov_18.078169 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 13 percent of BLAST hits supporting viral taxonomy 0.7111111111111111 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_330_length_136244_cov_18.078169 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142473 SAMEA13540507 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745947. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540507 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 22.8032 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 90 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_3506_length_32835_cov_13.463673 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7297297297297297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_3506_length_32835_cov_13.463673 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0335534 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142474 SAMEA13540508 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540508 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 616.679 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_3857_length_30419_cov_357.328851 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_3857_length_30419_cov_357.328851 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.3857 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142475 SAMEA13540509 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745947. BACPHLIP temperate score 0.13111098844285518 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540509 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 17.0946 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_4797_length_25309_cov_9.863705 Viral contig found in MAG ERR7745947_bin.351 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_4797_length_25309_cov_9.863705 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.93 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales;f__Monoglobaceae;g__UMGS1820;s__UMGS1820 sp900545865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.4797 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142476 SAMEA13540510 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade sp. virus assembled from ERR7745947. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540510 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 33.6565 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_558_length_104403_cov_19.165615 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_558_length_104403_cov_19.165615 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.558 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; UAG-readthrough crAss clade sp. virus enrichment approach none ERS11142477 SAMEA13540511 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745947. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540511 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 22.1516 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_6227_length_20138_cov_26.923234 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_6227_length_20138_cov_26.923234 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.3351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142478 SAMEA13540512 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7745947. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540512 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 13.8606 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_7715_length_16646_cov_7.816344 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_7715_length_16646_cov_7.816344 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738534_virus.4069 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11142479 SAMEA13540513 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745947. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540513 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 395.792 MAG coverage software Reads (ERR7745947) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567962) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_969_length_76576_cov_224.019020 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_20_1180__NODE_969_length_76576_cov_224.019020 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.410 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142480 SAMEA13540514 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745948. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540514 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 18.9622 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 84 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_32_length_218761_cov_11.056579_1 Viral contig found in MAG ERR7745948_bin.177 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_32_length_218761_cov_11.056579_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0349911 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142481 SAMEA13540515 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745948. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540515 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 49.6194 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_685_length_59024_cov_30.376932_1 Viral contig found in MAG ERR7745948_bin.60 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_685_length_59024_cov_30.376932_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745382_virus.1139 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142482 SAMEA13540516 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745948. BACPHLIP temperate score 0.09853065807331889 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540516 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 28.2975 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_1382_length_37973_cov_16.518340 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_1382_length_37973_cov_16.518340 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745922_virus.390 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142483 SAMEA13540517 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745948. BACPHLIP temperate score 0.4875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540517 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 12.0648 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_1734_length_32740_cov_6.935401 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_1734_length_32740_cov_6.935401 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745760_bin.144 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__CAG-238;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746344_virus.542 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142484 SAMEA13540518 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745948. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540518 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 12.9589 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_2200_length_27125_cov_7.565033 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_2200_length_27125_cov_7.565033 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0307965 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142485 SAMEA13540519 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7745948. BACPHLIP temperate score 0.1534374812512915 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540519 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 365.372 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_291_length_91927_cov_231.427022 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9574468085106383 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_291_length_91927_cov_231.427022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_virus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11142486 SAMEA13540520 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745948. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540520 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 29.1024 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_5247_length_13011_cov_17.334199 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_5247_length_13011_cov_17.334199 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.262 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745384_virus.4192 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142487 SAMEA13540521 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745948. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540521 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 17.4232 MAG coverage software Reads (ERR7745948) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559389) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 843 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_MoBio_hadza-I-L_O_18_2640__NODE_945_length_48607_cov_10.014692 Viral contig found in MAG ERR7745948_bin.26 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.78125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586344 sample name Hadza_MoBio_hadza-I-L_O_18_2640__NODE_945_length_48607_cov_10.014692 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.945 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142488 SAMEA13540522 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae provirus assembled from ERR7745951. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540522 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 24.1477 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1732_length_48219_cov_14.422666_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1732_length_48219_cov_14.422666_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098625 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A succinatutens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_provirus.1797 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11142489 SAMEA13540523 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745951. BACPHLIP temperate score 0.07637530562347188 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540523 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 21.5555 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2727_length_33823_cov_12.146032_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2727_length_33823_cov_12.146032_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_provirus.2727 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142490 SAMEA13540524 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745951. BACPHLIP temperate score 0.11745594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540524 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 15.7028 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 145 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_640_length_95677_cov_17.035356_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_640_length_95677_cov_17.035356_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_provirus.640 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142491 SAMEA13540525 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 0.02597739359623315 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540525 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 16.2759 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1014_length_71226_cov_9.136558 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1014_length_71226_cov_9.136558 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.201 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142492 SAMEA13540526 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540526 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 13.0766 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1359_length_57503_cov_7.405147 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1359_length_57503_cov_7.405147 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738627_virus.666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142493 SAMEA13540527 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 0.275 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540527 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 45.6642 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1824_length_46302_cov_33.124565 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5652173913043478 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_1824_length_46302_cov_33.124565 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.79 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142494 SAMEA13540528 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540528 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 25.6943 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2000_length_43229_cov_14.665044 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7096774193548387 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2000_length_43229_cov_14.665044 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.2000 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142495 SAMEA13540529 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540529 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:39Z INSDC last update 2022-12-27T01:22:39Z INSDC status public MAG coverage depth 12.2027 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2246_length_39299_cov_6.781704 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2246_length_39299_cov_6.781704 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.2054 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142496 SAMEA13540530 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745951. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540530 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 39.9854 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2504_length_36378_cov_22.595714 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6086956521739131 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2504_length_36378_cov_22.595714 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738568_bin.326 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__SFEL01;s__SFEL01 sp004557245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_provirus.614 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142497 SAMEA13540531 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 0.675 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540531 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 39.5073 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 604 Number of CRISPR spacer hits supporting host taxonomy 159 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2793_length_33179_cov_22.517340 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_2793_length_33179_cov_22.517340 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0365260 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142498 SAMEA13540532 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540532 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 7.40773 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 83 Number of CRISPR spacer hits supporting host taxonomy 97 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_3097_length_30248_cov_3.853899 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_3097_length_30248_cov_3.853899 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746345_bin.167 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-460;s__CAG-460 sp000437315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.3097 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142499 SAMEA13540533 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745951. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540533 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 5.11528 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_35024_length_3377_cov_2.813333 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_35024_length_3377_cov_2.813333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.35024 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142500 SAMEA13540534 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540534 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 8.12887 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_4658_length_21203_cov_4.513443 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_4658_length_21203_cov_4.513443 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_virus.1931 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142501 SAMEA13540535 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745951. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540535 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 7.54331 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_6366_length_15896_cov_4.093053 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_6366_length_15896_cov_4.093053 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745951_virus.6366 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142502 SAMEA13540536 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745951. BACPHLIP temperate score 0.11745594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540536 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 9.55803 MAG coverage software Reads (ERR7745951) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561784) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_G_8_1096__NODE_908_length_76866_cov_5.227910 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 20 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585520 sample name Hadza_MoBio_hadza-A-D_G_8_1096__NODE_908_length_76866_cov_5.227910 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.182 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-698;g__CAG-698;s__CAG-698 sp000431235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747128_virus.210 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142503 SAMEA13540537 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745953. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540537 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 15.0367 MAG coverage software Reads (ERR7745953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_C-REDO_B_9_1520__NODE_339_length_84981_cov_8.729706_1 Viral contig found in MAG ERR7745953_bin.145 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585776 sample name Hadza_MoBio_C-REDO_B_9_1520__NODE_339_length_84981_cov_8.729706_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738623_bin.157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.1368 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142504 SAMEA13540538 340016 uncultured virus This sample represents an uncultured Viruses provirus assembled from ERR7745953. BACPHLIP temperate score 0.01745594713656387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540538 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 27.2495 MAG coverage software Reads (ERR7745953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_C-REDO_B_9_1520__NODE_945_length_44343_cov_15.735937_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585776 sample name Hadza_MoBio_C-REDO_B_9_1520__NODE_945_length_44343_cov_15.735937_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_provirus.835 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11142505 SAMEA13540539 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745953. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540539 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 49.3683 MAG coverage software Reads (ERR7745953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_C-REDO_B_9_1520__NODE_1327_length_35574_cov_28.594219 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585776 sample name Hadza_MoBio_C-REDO_B_9_1520__NODE_1327_length_35574_cov_28.594219 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.1155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142506 SAMEA13540540 2100421 uncultured Caudovirales phage This sample represents an uncultured Picovirinae virus assembled from ERR7745953. BACPHLIP temperate score 0.0847458242767311 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540540 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 10.3671 MAG coverage software Reads (ERR7745953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_B_9_1520__NODE_2609_length_21342_cov_5.906701 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585776 sample name Hadza_MoBio_C-REDO_B_9_1520__NODE_2609_length_21342_cov_5.906701 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.5756 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae; Picovirinae virus enrichment approach none ERS11142507 SAMEA13540541 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745953. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540541 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 16.7238 MAG coverage software Reads (ERR7745953) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561484) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 228 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_C-REDO_B_9_1520__NODE_547_length_63777_cov_9.414097 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9487179487179488 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585776 sample name Hadza_MoBio_C-REDO_B_9_1520__NODE_547_length_63777_cov_9.414097 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_virus.423 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142508 SAMEA13540542 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745963. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540542 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 208.684 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 773 Number of CRISPR spacer hits supporting host taxonomy 291 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_108_length_193356_cov_125.053669_1 Viral contig found in MAG ERR7745963_bin.406 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_108_length_193356_cov_125.053669_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738626_bin.272 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745613_provirus.67 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142509 SAMEA13540543 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745963. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540543 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 17.7013 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 68 Number of CRISPR spacer hits supporting host taxonomy 268 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1801_length_46772_cov_10.909391_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7586206896551724 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1801_length_46772_cov_10.909391_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0272411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142510 SAMEA13540544 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745963. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540544 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 33.1798 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 27 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_330_length_122091_cov_20.701993_1 Viral contig found in MAG ERR7745963_bin.190 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_330_length_122091_cov_20.701993_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME266586 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-180;s__CAG-180 sp000432435 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738150_provirus.859 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142511 SAMEA13540545 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745963. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540545 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 20.2924 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_762_length_77163_cov_12.679358_1 Viral contig found in MAG ERR7745963_bin.133 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_762_length_77163_cov_12.679358_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_provirus.762 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142512 SAMEA13540546 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745963. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540546 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 39.7629 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1297_length_57340_cov_24.290135 Viral contig found in MAG ERR7745963_bin.171 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6216216216216216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1297_length_57340_cov_24.290135 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.1297 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142513 SAMEA13540547 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745963. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540547 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 16.4628 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1562_length_51154_cov_10.055230 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 68.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6451612903225806 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1562_length_51154_cov_10.055230 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.1562 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142514 SAMEA13540548 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745963. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540548 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 10.0027 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1554 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1836_length_46129_cov_5.951880 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_1836_length_46129_cov_5.951880 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.1836 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142515 SAMEA13540549 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745963. BACPHLIP temperate score 0.8375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540549 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 209.051 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 504 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2028_length_43384_cov_126.294756 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2028_length_43384_cov_126.294756 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738150_virus.405 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142516 SAMEA13540550 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745963. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540550 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 13.9392 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_219_length_146897_cov_8.378048 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_219_length_146897_cov_8.378048 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.219 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142517 SAMEA13540551 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745963. BACPHLIP temperate score 0.02241189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540551 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 21.0485 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 273 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2383_length_38766_cov_12.827548 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2383_length_38766_cov_12.827548 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.1195 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142518 SAMEA13540552 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745963. BACPHLIP temperate score 0.6 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540552 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 16.0071 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2673_length_35912_cov_9.720050 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.44 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2673_length_35912_cov_9.720050 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745963_virus.2673 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142519 SAMEA13540553 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7745963. BACPHLIP temperate score 0.08869765791341377 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540553 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 18.8913 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 476 Number of CRISPR spacer hits supporting host taxonomy 568 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2946_length_33596_cov_11.533309 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4516129032258064 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_2946_length_33596_cov_11.533309 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11142520 SAMEA13540554 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745963. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540554 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 6.7601 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_3540_length_29458_cov_3.837684 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_3540_length_29458_cov_3.837684 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_provirus.514 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142521 SAMEA13540555 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745963. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540555 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 21.8377 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_442_length_104144_cov_13.116156 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.9078947368421052 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_442_length_104144_cov_13.116156 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.368 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142522 SAMEA13540556 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745963. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540556 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 6.63722 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_5409_length_21535_cov_3.838895 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_5409_length_21535_cov_3.838895 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.1803 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142523 SAMEA13540557 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745963. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540557 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 69.6954 MAG coverage software Reads (ERR7745963) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567841) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_78497_length_2550_cov_44.353013 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586161 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_6_2233__NODE_78497_length_2550_cov_44.353013 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.13523 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142524 SAMEA13540558 340016 uncultured virus This sample represents an uncultured Viruses provirus assembled from ERR7745967. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540558 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 82.7773 MAG coverage software Reads (ERR7745967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_C-REDO_E_3_1554__NODE_24_length_176691_cov_47.699780_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585808 sample name Hadza_MoBio_C-REDO_E_3_1554__NODE_24_length_176691_cov_47.699780_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738657_provirus.203 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11142525 SAMEA13540559 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745967. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540559 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 260.492 MAG coverage software Reads (ERR7745967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 78 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_C-REDO_E_3_1554__NODE_673_length_42890_cov_153.482610_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585808 sample name Hadza_MoBio_C-REDO_E_3_1554__NODE_673_length_42890_cov_153.482610_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746757_provirus.936 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142526 SAMEA13540560 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745967. BACPHLIP temperate score 0.08312057094440387 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540560 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 21.2702 MAG coverage software Reads (ERR7745967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_C-REDO_E_3_1554__NODE_1669_length_22926_cov_12.342991 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585808 sample name Hadza_MoBio_C-REDO_E_3_1554__NODE_1669_length_22926_cov_12.342991 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142527 SAMEA13540561 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745967. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540561 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 180.081 MAG coverage software Reads (ERR7745967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 107 Submitter Id Hadza_MoBio_C-REDO_E_3_1554__NODE_342_length_61887_cov_103.745996 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; HMM-based (lower-bound) completeness score 72.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.35294117647058826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585808 sample name Hadza_MoBio_C-REDO_E_3_1554__NODE_342_length_61887_cov_103.745996 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745967_virus.342 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142528 SAMEA13540562 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745967. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540562 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 11.6702 MAG coverage software Reads (ERR7745967) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560928) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 50 Number of CRISPR spacer hits supporting host taxonomy 80 Submitter Id Hadza_MoBio_C-REDO_E_3_1554__NODE_662_length_43357_cov_6.635305 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585808 sample name Hadza_MoBio_C-REDO_E_3_1554__NODE_662_length_43357_cov_6.635305 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738147_virus.298 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142529 SAMEA13540563 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745970. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540563 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 21.3285 MAG coverage software Reads (ERR7745970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559772) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 99 Submitter Id Hadza_MoBio_hadza-E-H_P_22_2354__NODE_336_length_81211_cov_12.470210_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586221 sample name Hadza_MoBio_hadza-E-H_P_22_2354__NODE_336_length_81211_cov_12.470210_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142530 SAMEA13540564 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7745970. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540564 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 41.0206 MAG coverage software Reads (ERR7745970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559772) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_P_22_2354__NODE_11700_length_5402_cov_25.069484 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586221 sample name Hadza_MoBio_hadza-E-H_P_22_2354__NODE_11700_length_5402_cov_25.069484 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746757_bin.199 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436;s__UBA1436 sp900541355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.11700 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142531 SAMEA13540565 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7745970. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540565 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 6.29701 MAG coverage software Reads (ERR7745970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559772) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_P_22_2354__NODE_1468_length_32371_cov_3.386357 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586221 sample name Hadza_MoBio_hadza-E-H_P_22_2354__NODE_1468_length_32371_cov_3.386357 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018425 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__CAG-791 sp000431495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.582 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11142532 SAMEA13540566 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7745970. BACPHLIP temperate score 0.00991189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540566 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 9.58111 MAG coverage software Reads (ERR7745970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559772) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_P_22_2354__NODE_3045_length_17200_cov_5.561350 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586221 sample name Hadza_MoBio_hadza-E-H_P_22_2354__NODE_3045_length_17200_cov_5.561350 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.3045 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142533 SAMEA13540567 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745970. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540567 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 9.70788 MAG coverage software Reads (ERR7745970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559772) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 157 Submitter Id Hadza_MoBio_hadza-E-H_P_22_2354__NODE_577_length_59820_cov_5.670271 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586221 sample name Hadza_MoBio_hadza-E-H_P_22_2354__NODE_577_length_59820_cov_5.670271 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738568_virus.1165 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142534 SAMEA13540568 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745970. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540568 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 13.9809 MAG coverage software Reads (ERR7745970) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559772) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_22_2354__NODE_853_length_47185_cov_7.747071 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586221 sample name Hadza_MoBio_hadza-E-H_P_22_2354__NODE_853_length_47185_cov_7.747071 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738173_bin.31 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFFH01;s__SFFH01 sp900542445 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745970_virus.853 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142535 SAMEA13540569 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745975. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540569 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 237.686 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_1167_length_64025_cov_138.506208_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_1167_length_64025_cov_138.506208_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_provirus.854 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142536 SAMEA13540570 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745975. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540570 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 13.8597 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_148_length_181911_cov_7.731233_1 Viral contig found in MAG ERR7745975_bin.215 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_148_length_181911_cov_7.731233_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001052 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317;s__CAG-317 sp000433215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_provirus.148 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142537 SAMEA13540571 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745975. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540571 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 184.635 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2143_length_44168_cov_116.751650_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2143_length_44168_cov_116.751650_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_provirus.1146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142538 SAMEA13540572 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745975. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540572 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 53.3568 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 350 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_272_length_138457_cov_43.388394_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_272_length_138457_cov_43.388394_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.191 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142539 SAMEA13540573 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7745975. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540573 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 81.0302 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_42_length_292727_cov_47.094639_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.5616438356164384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_42_length_292727_cov_47.094639_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_provirus.62 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11142540 SAMEA13540574 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745975. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540574 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 51.2188 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 141 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_769_length_81474_cov_31.804170_1 Viral contig found in MAG ERR7745975_bin.40 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_769_length_81474_cov_31.804170_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_provirus.917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142541 SAMEA13540575 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745975. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540575 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 14.5124 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_11148_length_12929_cov_8.261671 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_11148_length_12929_cov_8.261671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.9454 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142542 SAMEA13540576 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745975. BACPHLIP temperate score 0.08243392070484583 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540576 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 366.074 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_145_length_183584_cov_210.504591 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 16 number of unique standard tRNAs extracted 14 percent of BLAST hits supporting viral taxonomy 0.5849056603773585 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_145_length_183584_cov_210.504591 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_virus.17 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142543 SAMEA13540577 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745975. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540577 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 37.8935 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_1868_length_48558_cov_21.462614 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_1868_length_48558_cov_21.462614 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_virus.1868 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142544 SAMEA13540578 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745975. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540578 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 14.0375 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2104_length_44838_cov_8.050446 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2104_length_44838_cov_8.050446 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.1695 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142545 SAMEA13540579 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745975. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540579 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:37Z INSDC last update 2022-12-27T01:22:37Z INSDC status public MAG coverage depth 20.026 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2340_length_41953_cov_11.341699 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2340_length_41953_cov_11.341699 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738561_bin.41 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UBA1191;s__UBA1191 sp900066305 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_virus.2340 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142546 SAMEA13540580 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745975. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540580 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 21.0498 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2552_length_39883_cov_12.032684 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2552_length_39883_cov_12.032684 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.1515 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142547 SAMEA13540581 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745975. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540581 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 30.4216 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2745_length_38116_cov_17.280659 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8214285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_2745_length_38116_cov_17.280659 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_virus.2745 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142548 SAMEA13540582 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu virus assembled from ERR7745975. BACPHLIP temperate score 0.18548688392358637 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540582 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 28.7536 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_3080_length_35518_cov_16.346745 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_3080_length_35518_cov_16.346745 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.2054 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11142549 SAMEA13540583 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745975. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540583 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 64.8749 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 125 Number of CRISPR spacer hits supporting host taxonomy 120 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_3424_length_32966_cov_40.123962 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_3424_length_32966_cov_40.123962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_virus.503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142550 SAMEA13540584 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745975. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540584 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 614.54 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 450 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_3777_length_30956_cov_355.853817 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_3777_length_30956_cov_355.853817 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745559_virus.891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142551 SAMEA13540585 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745975. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540585 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 35.418 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_429_length_110210_cov_20.030291 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6792452830188679 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_429_length_110210_cov_20.030291 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019375 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R;s__Eubacterium_R sp000436835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_provirus.252 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142552 SAMEA13540586 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745975. BACPHLIP temperate score 0.06452230274393414 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540586 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 8.81198 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_5628_length_22743_cov_4.970529 Viral contig found in MAG ERR7745975_bin.309 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_5628_length_22743_cov_4.970529 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_provirus.1099 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142553 SAMEA13540587 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745975. BACPHLIP temperate score 0.5625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540587 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 38.572 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 93 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_6406_length_20543_cov_22.063129 Viral contig found in MAG ERR7745975_bin.302 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_6406_length_20543_cov_22.063129 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.5792 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142554 SAMEA13540588 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745975. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540588 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 57.0181 MAG coverage software Reads (ERR7745975) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567797) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_851_length_76690_cov_33.053607 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 86.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_18_1662__NODE_851_length_76690_cov_33.053607 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746051_bin.216 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger variabilis_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142555 SAMEA13540589 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745985. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540589 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 83.5207 MAG coverage software Reads (ERR7745985) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567256) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 143 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_94_length_151936_cov_51.376757_1 Viral contig found in MAG ERR7745985_bin.64 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.13 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787378 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_94_length_151936_cov_51.376757_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0350419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142556 SAMEA13540590 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745985. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540590 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 31.2474 MAG coverage software Reads (ERR7745985) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567256) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_1198_length_34569_cov_20.985910 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787378 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_1198_length_34569_cov_20.985910 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745985_virus.1198 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142557 SAMEA13540591 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745985. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540591 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 158.11 MAG coverage software Reads (ERR7745985) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567256) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_189_length_108518_cov_96.018268 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8235294117647058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787378 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_189_length_108518_cov_96.018268 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738265_bin.79 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp900540255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738472_virus.372 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142558 SAMEA13540592 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745985. BACPHLIP temperate score 0.03714174109185703 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540592 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 14.881 MAG coverage software Reads (ERR7745985) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567256) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_3618_length_13674_cov_8.972126 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787378 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_3618_length_13674_cov_8.972126 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159485 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745985_virus.3618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142559 SAMEA13540593 1701671 uncultured podovirus This sample represents an uncultured Bordetella virus BPP1 virus assembled from ERR7745985. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540593 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 48.0334 MAG coverage software Reads (ERR7745985) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567256) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_606_length_56104_cov_29.052261 Viral contig found in MAG ERR7745985_bin.143 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.43478260869565216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787378 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_606_length_56104_cov_29.052261 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747782_bin.309 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus;s__Duodenibacillus sp900544255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745985_virus.606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Rauchvirus; Bordetella virus BPP1 virus enrichment approach none ERS11142560 SAMEA13540594 2133760 Siphoviridae environmental samples This sample represents an uncultured Clostridium phage phi8074-B1 virus assembled from ERR7745985. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540594 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 239.731 MAG coverage software Reads (ERR7745985) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567256) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_811_length_46449_cov_146.352411 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2016 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Nepal geographic location (elevation) 1400 geographic location (latitude) 28.17 geographic location (longitude) 84.25 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1371/journal.pbio.2005396 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1371/journal.pbio.2005396 sample collection device or method https://doi.org/10.1371/journal.pbio.2005396 sample derived from ERS2787378 sample name Nepal_MoBio_Fiber-Hadza-Nepal_B_1_RAJ1011YZ__NODE_811_length_46449_cov_146.352411 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.212 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia;s__Romboutsia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745985_virus.811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Clostridium phage phi8074-B1 virus enrichment approach none ERS11142561 SAMEA13540595 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745989. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540595 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 18.1182 MAG coverage software Reads (ERR7745989) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_C-REDO_F_3_1566__NODE_1210_length_37194_cov_10.255220_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8709677419354839 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585820 sample name Hadza_MoBio_C-REDO_F_3_1566__NODE_1210_length_37194_cov_10.255220_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_provirus.1478 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142562 SAMEA13540596 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745989. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540596 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 9.98106 MAG coverage software Reads (ERR7745989) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_C-REDO_F_3_1566__NODE_433_length_69058_cov_5.374060_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585820 sample name Hadza_MoBio_C-REDO_F_3_1566__NODE_433_length_69058_cov_5.374060_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745414_provirus.156 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142563 SAMEA13540597 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745989. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540597 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 16.7208 MAG coverage software Reads (ERR7745989) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_C-REDO_F_3_1566__NODE_1012_length_40946_cov_9.506790 Viral contig found in MAG ERR7745989_bin.225 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585820 sample name Hadza_MoBio_C-REDO_F_3_1566__NODE_1012_length_40946_cov_9.506790 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_virus.1703 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142564 SAMEA13540598 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745989. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540598 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 12.8853 MAG coverage software Reads (ERR7745989) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_C-REDO_F_3_1566__NODE_1331_length_34951_cov_7.108276 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585820 sample name Hadza_MoBio_C-REDO_F_3_1566__NODE_1331_length_34951_cov_7.108276 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745963_bin.410 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp001916075 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_virus.1331 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142565 SAMEA13540599 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745989. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540599 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 39.6378 MAG coverage software Reads (ERR7745989) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_C-REDO_F_3_1566__NODE_1937_length_27710_cov_23.217855 Viral contig found in MAG ERR7745989_bin.204 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585820 sample name Hadza_MoBio_C-REDO_F_3_1566__NODE_1937_length_27710_cov_23.217855 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.1125 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142566 SAMEA13540600 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745989. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540600 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 7.89571 MAG coverage software Reads (ERR7745989) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_C-REDO_F_3_1566__NODE_3352_length_18828_cov_4.231188 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585820 sample name Hadza_MoBio_C-REDO_F_3_1566__NODE_3352_length_18828_cov_4.231188 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_provirus.1146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142567 SAMEA13540601 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745989. BACPHLIP temperate score 0.3875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540601 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 12.722 MAG coverage software Reads (ERR7745989) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566954) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 291 Submitter Id Hadza_MoBio_C-REDO_F_3_1566__NODE_628_length_55221_cov_7.154795 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585820 sample name Hadza_MoBio_C-REDO_F_3_1566__NODE_628_length_55221_cov_7.154795 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_virus.391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142568 SAMEA13540602 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7745990. BACPHLIP temperate score 0.09471365638766524 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540602 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 233.244 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1036_length_73573_cov_140.019919_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1036_length_73573_cov_140.019919_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME023798 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900543155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_provirus.1656 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142569 SAMEA13540603 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7745990. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540603 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 27.9127 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1559_length_58071_cov_16.748284_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1559_length_58071_cov_16.748284_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_provirus.1559 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142570 SAMEA13540604 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7745990. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540604 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 12.1091 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_217_length_156139_cov_6.978547_1 Viral contig found in MAG ERR7745990_bin.158 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_217_length_156139_cov_6.978547_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_provirus.217 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11142571 SAMEA13540605 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745990. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540605 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 26.2577 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_394_length_125162_cov_15.233649_1 Viral contig found in MAG ERR7745990_bin.188 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_394_length_125162_cov_15.233649_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_provirus.979 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142572 SAMEA13540606 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745990. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540606 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 88.9717 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 88 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_766_length_88459_cov_51.632832_1 Viral contig found in MAG ERR7745990_bin.94 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_766_length_88459_cov_51.632832_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_provirus.273 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142573 SAMEA13540607 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540607 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 60.8181 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1236_length_66342_cov_35.861345 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.36 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1236_length_66342_cov_35.861345 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.462 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__UBA1232;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.1236 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142574 SAMEA13540608 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540608 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 8.84226 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 99 Number of CRISPR spacer hits supporting host taxonomy 1230 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1400_length_61631_cov_5.003932 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6410256410256411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1400_length_61631_cov_5.003932 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142575 SAMEA13540609 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540609 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 263.768 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_160_length_178634_cov_151.544314 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 58.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_160_length_178634_cov_151.544314 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737970_virus.45 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142576 SAMEA13540610 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745990. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540610 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 37.9771 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 26 Number of CRISPR spacer hits supporting host taxonomy 140 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1950_length_50434_cov_22.038942 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4642857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_1950_length_50434_cov_22.038942 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253778 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp003491505 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_virus.1551 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142577 SAMEA13540611 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.175 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540611 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 25.643 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 57 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_2192_length_46775_cov_15.132896 Viral contig found in MAG ERR7745990_bin.84 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 84.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_2192_length_46775_cov_15.132896 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_virus.1099 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142578 SAMEA13540612 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745990. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540612 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 21.1438 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_2508_length_42383_cov_12.856025 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_2508_length_42383_cov_12.856025 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.2508 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142579 SAMEA13540613 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540613 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 9.6297 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_2928_length_38122_cov_5.595689 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_2928_length_38122_cov_5.595689 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.2928 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142580 SAMEA13540614 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll virus assembled from ERR7745990. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540614 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 33.158 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_3151_length_36021_cov_19.675968 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_3151_length_36021_cov_19.675968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME284285 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194;s__CAG-194 sp000432915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745845_virus.2255 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11142581 SAMEA13540615 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7745990. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540615 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 187.293 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_3758_length_31196_cov_108.879109 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_3758_length_31196_cov_108.879109 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_virus.631 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11142582 SAMEA13540616 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745990. BACPHLIP temperate score 0.07720665318800916 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540616 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 11.0485 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 151 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_4658_length_25986_cov_6.344784 Viral contig found in MAG ERR7745990_bin.73 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_4658_length_25986_cov_6.344784 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142583 SAMEA13540617 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.1264047273878133 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540617 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 8.34553 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_5424_length_22773_cov_4.683909 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.21 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_5424_length_22773_cov_4.683909 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME269197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615;s__KLE1615 sp900066985 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.5424 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142584 SAMEA13540618 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540618 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 13.5904 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 123 Number of CRISPR spacer hits supporting host taxonomy 196 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_655_length_96473_cov_7.843074 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.2631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_655_length_96473_cov_7.843074 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745990_virus.655 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142585 SAMEA13540619 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7745990. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540619 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 13.3397 MAG coverage software Reads (ERR7745990) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559405) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-I-L_K_14_2624__NODE_80_length_247842_cov_8.147164 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9210526315789472 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586333 sample name Hadza_MoBio_hadza-I-L_K_14_2624__NODE_80_length_247842_cov_8.147164 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.224 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__Ruminococcus sp900540005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1936415 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142586 SAMEA13540620 2133760 Siphoviridae environmental samples This sample represents an uncultured Psavirus provirus assembled from ERR7745994. BACPHLIP temperate score 0.130873179909068 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540620 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 11.0362 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1519_length_48696_cov_6.079845_1 Viral contig found in MAG ERR7745994_bin.199 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1519_length_48696_cov_6.079845_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_provirus.1519 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Psavirus virus enrichment approach none ERS11142587 SAMEA13540621 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745994. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540621 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 20.8453 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_2648_length_32474_cov_12.307251_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_2648_length_32474_cov_12.307251_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_provirus.1783 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142588 SAMEA13540622 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7745994. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540622 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 11.9204 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_611_length_88277_cov_6.926610_1 Viral contig found in MAG ERR7745994_bin.69 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_611_length_88277_cov_6.926610_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME277097 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02;s__F23-B02 sp003533405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_provirus.611 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142589 SAMEA13540623 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745994. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540623 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 35.1854 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 242 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1024_length_64347_cov_21.420134 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1024_length_64347_cov_21.420134 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745603_virus.118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142590 SAMEA13540624 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7745994. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540624 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 30.0364 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 427 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1528_length_48523_cov_17.040395 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1528_length_48523_cov_17.040395 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0314473 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11142591 SAMEA13540625 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7745994. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540625 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 16.258 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_177_length_170383_cov_9.057426 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 20 number of unique standard tRNAs extracted 17 percent of BLAST hits supporting viral taxonomy 0.5614035087719298 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_177_length_170383_cov_9.057426 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.256 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142592 SAMEA13540626 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745994. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540626 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 237.641 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 211 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1979_length_40471_cov_134.520473 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_1979_length_40471_cov_134.520473 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME246707 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__Phil1;s__Phil1 sp001940855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.1979 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142593 SAMEA13540627 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745994. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540627 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 21.5114 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_222_length_148408_cov_12.203410 Viral contig found in MAG ERR7745994_bin.342 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_222_length_148408_cov_12.203410 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.222 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142594 SAMEA13540628 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7745994. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540628 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 9.69094 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_2570_length_33111_cov_5.334716 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_2570_length_33111_cov_5.334716 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0351188 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142595 SAMEA13540629 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745994. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540629 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 9.27083 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_3037_length_29338_cov_5.048529 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_3037_length_29338_cov_5.048529 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.3037 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142596 SAMEA13540630 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7745994. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540630 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 20.0424 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 50 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_357_length_118783_cov_11.545297 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 67.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.7045454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_357_length_118783_cov_11.545297 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.357 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142597 SAMEA13540631 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745994. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540631 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 40.7899 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_4146_length_23366_cov_23.192494 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_4146_length_23366_cov_23.192494 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.4146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142598 SAMEA13540632 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745994. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540632 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 6.65118 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_4742_length_21138_cov_3.512464 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_4742_length_21138_cov_3.512464 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738240_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__Firm-11;s__Firm-11 sp900548145 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.4742 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142599 SAMEA13540633 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745994. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540633 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 32.4424 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_5668_length_18367_cov_19.775123 Viral contig found in MAG ERR7745994_bin.310 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_5668_length_18367_cov_19.775123 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.5668 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142600 SAMEA13540634 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7745994. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540634 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 29.4612 MAG coverage software Reads (ERR7745994) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560700) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 118 Submitter Id Hadza_MoBio_hadza-E-H_E_1_1719__NODE_782_length_76920_cov_17.621241 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585962 sample name Hadza_MoBio_hadza-E-H_E_1_1719__NODE_782_length_76920_cov_17.621241 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.782 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142601 SAMEA13540635 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746009. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540635 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 38.3729 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_11_length_329520_cov_16.908904_1 Viral contig found in MAG ERR7746009_bin.108 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8809523809523809 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_11_length_329520_cov_16.908904_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.1313 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142602 SAMEA13540636 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746009. BACPHLIP temperate score 0.10192912905635668 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540636 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 206.636 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_38_length_213569_cov_104.105376_1 Viral contig found in MAG ERR7746009_bin.23 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8387096774193549 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_38_length_213569_cov_104.105376_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001423 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0269416 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142603 SAMEA13540637 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746009. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540637 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 68.2295 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 282 Number of CRISPR spacer hits supporting host taxonomy 444 Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_97_length_146092_cov_34.424977_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_97_length_146092_cov_34.424977_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142522 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium adolescentis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746009_provirus.97 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142604 SAMEA13540638 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746009. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13540638 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-28T19:46:21Z INSDC status public MAG coverage depth 10.2131 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 88 Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_1523_length_25311_cov_4.696838 Viral contig found in MAG ERR7746009_bin.19 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.7 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_1523_length_25311_cov_4.696838 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila;s__Bilophila wadsworthia vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746009_virus.1523 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142605 SAMEA13540639 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746009. BACPHLIP temperate score 0.04408093884155772 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540639 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:36Z INSDC last update 2022-12-27T01:22:36Z INSDC status public MAG coverage depth 39.942 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_2588_length_16455_cov_20.858275 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_2588_length_16455_cov_20.858275 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0129098 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142606 SAMEA13540640 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746009. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13540640 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-28T19:46:22Z INSDC status public MAG coverage depth 43.7631 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_52_length_183425_cov_20.139560 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.5365853658536586 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_52_length_183425_cov_20.139560 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746009_virus.52 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142607 SAMEA13540641 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 virus assembled from ERR7746009. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540641 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 4725.38 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 764 Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_755_length_44265_cov_2412.581063 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9245283018867924 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_755_length_44265_cov_2412.581063 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0315891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11142608 SAMEA13540642 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746009. BACPHLIP temperate score 0.10495594713656388 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540642 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 291.991 MAG coverage software Reads (ERR7746009) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_C-REDO_C_5_1529__NODE_973_length_36116_cov_150.554399 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6842105263157895 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585784 sample name Hadza_MoBio_C-REDO_C_5_1529__NODE_973_length_36116_cov_150.554399 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0248554 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142609 SAMEA13540643 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7746012. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540643 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 8.59289 MAG coverage software Reads (ERR7746012) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559707) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 154 Number of CRISPR spacer hits supporting host taxonomy 75 Submitter Id Hadza_MoBio_hadza-E-H_P_14_2348__NODE_282_length_79647_cov_5.078861_1 Viral contig found in MAG ERR7746012_bin.63 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586218 sample name Hadza_MoBio_hadza-E-H_P_14_2348__NODE_282_length_79647_cov_5.078861_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_provirus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11142610 SAMEA13540644 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746012. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540644 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 102.803 MAG coverage software Reads (ERR7746012) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559707) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 277 Submitter Id Hadza_MoBio_hadza-E-H_P_14_2348__NODE_78_length_137311_cov_101.451718_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.88 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586218 sample name Hadza_MoBio_hadza-E-H_P_14_2348__NODE_78_length_137311_cov_101.451718_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142611 SAMEA13540645 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746012. BACPHLIP temperate score 0.7824339207048457 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540645 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.2465 MAG coverage software Reads (ERR7746012) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559707) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_P_14_2348__NODE_1239_length_33939_cov_6.626307 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586218 sample name Hadza_MoBio_hadza-E-H_P_14_2348__NODE_1239_length_33939_cov_6.626307 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745414_bin.186 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900768625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1127389 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142612 SAMEA13540646 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746012. BACPHLIP temperate score 0.01693336174904671 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540646 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.2643 MAG coverage software Reads (ERR7746012) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559707) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_P_14_2348__NODE_1493_length_29711_cov_6.486569 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586218 sample name Hadza_MoBio_hadza-E-H_P_14_2348__NODE_1493_length_29711_cov_6.486569 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.1937 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142613 SAMEA13540647 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7746012. BACPHLIP temperate score 0.00991189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540647 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 22.2587 MAG coverage software Reads (ERR7746012) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559707) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_P_14_2348__NODE_185_length_98060_cov_12.956054 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.935064935064935 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586218 sample name Hadza_MoBio_hadza-E-H_P_14_2348__NODE_185_length_98060_cov_12.956054 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11142614 SAMEA13540648 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746012. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540648 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.3365 MAG coverage software Reads (ERR7746012) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559707) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-E-H_P_14_2348__NODE_656_length_50722_cov_6.540014 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586218 sample name Hadza_MoBio_hadza-E-H_P_14_2348__NODE_656_length_50722_cov_6.540014 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738238_provirus.170 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142615 SAMEA13540649 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746030. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540649 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 9.1388 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1249_length_58664_cov_5.132009_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 57.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1249_length_58664_cov_5.132009_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746365_bin.336 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.64 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142616 SAMEA13540650 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746030. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540650 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 25.3608 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_247_length_155333_cov_14.099036_1 Viral contig found in MAG ERR7746030_bin.183 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_247_length_155333_cov_14.099036_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_virus.2332 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142617 SAMEA13540651 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746030. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540651 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 129.859 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_43_length_328355_cov_71.989768_1 Viral contig found in MAG ERR7746030_bin.313 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_43_length_328355_cov_71.989768_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.2611 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142618 SAMEA13540652 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7746030. BACPHLIP temperate score 0.6649779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540652 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 93.5117 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 126 Number of CRISPR spacer hits supporting host taxonomy 835 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_731_length_84827_cov_59.373782_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8484848484848485 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_731_length_84827_cov_59.373782_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_provirus.731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142619 SAMEA13540653 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746030. BACPHLIP temperate score 0.1424559471365639 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540653 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 14.6505 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1190_length_60869_cov_8.263982 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1190_length_60869_cov_8.263982 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_virus.1376 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142620 SAMEA13540654 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746030. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540654 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 19.4751 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 439 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1566_length_50911_cov_11.193650 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 75.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1566_length_50911_cov_11.193650 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746365_bin.336 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.1566 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142621 SAMEA13540655 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746030. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540655 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.5234 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1909_length_44092_cov_6.530819 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_1909_length_44092_cov_6.530819 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745613_bin.13 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia;s__Marvinbryantia sp014385005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.1909 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142622 SAMEA13540656 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746030. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540656 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.3879 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_2081_length_41405_cov_6.281673 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_2081_length_41405_cov_6.281673 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738571_bin.392 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__UBA644;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.2081 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142623 SAMEA13540657 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746030. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540657 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 84.7393 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 111 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_2407_length_36906_cov_47.755519 Viral contig found in MAG ERR7746030_bin.295 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_2407_length_36906_cov_47.755519 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745563_virus.395 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142624 SAMEA13540658 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746030. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540658 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 15.7178 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_2796_length_32672_cov_8.821506 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_2796_length_32672_cov_8.821506 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738192_bin.62 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732;s__UBA9732 sp001940825 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738213_provirus.55 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142625 SAMEA13540659 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746030. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540659 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 22.3414 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_3828_length_25300_cov_12.529913 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_3828_length_25300_cov_12.529913 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NK3B98;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.3828 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142626 SAMEA13540660 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746030. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540660 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 13.9054 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_5154_length_19615_cov_7.715733 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_5154_length_19615_cov_7.715733 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.5154 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142627 SAMEA13540661 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746030. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540661 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 21.1093 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_6811_length_15262_cov_11.906223 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_6811_length_15262_cov_11.906223 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.6811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142628 SAMEA13540662 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746030. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540662 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 12.9236 MAG coverage software Reads (ERR7746030) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560629) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-A-D_J_18_1660__NODE_950_length_71687_cov_7.237271 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585903 sample name Hadza_MoBio_hadza-A-D_J_18_1660__NODE_950_length_71687_cov_7.237271 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.950 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142629 SAMEA13540663 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746048. BACPHLIP temperate score 0.864977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540663 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 352.457 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 175 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_331_length_110322_cov_208.444673_1 Viral contig found in MAG ERR7746048_bin.132 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_331_length_110322_cov_208.444673_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024079 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436035 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_provirus.117 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142630 SAMEA13540664 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746048. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540664 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 31.0204 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 158 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_677_length_73421_cov_19.350172_1 Viral contig found in MAG ERR7746048_bin.102 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_677_length_73421_cov_19.350172_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.677 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142631 SAMEA13540665 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746048. BACPHLIP temperate score 0.12932322959045642 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540665 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 22.0845 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 194 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_1035_length_56934_cov_12.497265 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7741935483870968 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_1035_length_56934_cov_12.497265 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_virus.1035 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142632 SAMEA13540666 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7746048. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540666 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 35.4755 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 573 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_1447_length_46316_cov_20.388373 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_1447_length_46316_cov_20.388373 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001115 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_E vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_virus.1447 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11142633 SAMEA13540667 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746048. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540667 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 44.7978 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_1720_length_41665_cov_25.798476 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_1720_length_41665_cov_25.798476 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_virus.1720 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142634 SAMEA13540668 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746048. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540668 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.8906 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_202_length_136061_cov_6.716967 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.96875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_202_length_136061_cov_6.716967 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_virus.202 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142635 SAMEA13540669 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746048. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540669 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 18.3897 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_235_length_128125_cov_10.531504 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6964285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_235_length_128125_cov_10.531504 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_virus.235 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142636 SAMEA13540670 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746048. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540670 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 44.7643 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 855 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_353_length_106551_cov_26.349278 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_353_length_106551_cov_26.349278 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.247 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142637 SAMEA13540671 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746048. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540671 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 7.21435 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_4363_length_21993_cov_3.884787 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_4363_length_21993_cov_3.884787 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738595_provirus.1146 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142638 SAMEA13540672 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746048. BACPHLIP temperate score 0.04588790558384566 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540672 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 38.4306 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_5954_length_17379_cov_21.990232 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_5954_length_17379_cov_21.990232 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745890_bin.370 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__W2P13-069;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_virus.5954 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142639 SAMEA13540673 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746048. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540673 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 251.678 MAG coverage software Reads (ERR7746048) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561940) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_G_7_1734__NODE_7743_length_14069_cov_145.278241 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585977 sample name Hadza_MoBio_hadza-E-H_G_7_1734__NODE_7743_length_14069_cov_145.278241 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745816_bin.141 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_virus.7743 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142640 SAMEA13540674 2133760 Siphoviridae environmental samples This sample represents an uncultured Phifelvirus provirus assembled from ERR7746051. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540674 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 24.7682 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 190 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1127_length_48527_cov_18.198452_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1127_length_48527_cov_18.198452_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_provirus.1127 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Phifelvirus virus enrichment approach none ERS11142641 SAMEA13540675 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746051. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540675 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 21.0258 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_259_length_98075_cov_11.945693_1 Viral contig found in MAG ERR7746051_bin.186 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_259_length_98075_cov_11.945693_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_provirus.259 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142642 SAMEA13540676 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746051. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540676 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 28.0186 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_632_length_64927_cov_16.524827_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_632_length_64927_cov_16.524827_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142643 SAMEA13540677 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746051. BACPHLIP temperate score 0.275 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540677 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 18.6749 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_845_length_57126_cov_10.954916_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_845_length_57126_cov_10.954916_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125893 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger formicilis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746048_provirus.595 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142644 SAMEA13540678 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746051. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540678 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 25.9157 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1179_length_47208_cov_15.268104 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6216216216216216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1179_length_47208_cov_15.268104 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.1179 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142645 SAMEA13540679 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540679 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 348.509 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1276_length_45080_cov_193.515166 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4772727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1276_length_45080_cov_193.515166 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.1276 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142646 SAMEA13540680 2133760 Siphoviridae environmental samples This sample represents an uncultured Clostridium phage phi8074-B1 virus assembled from ERR7746051. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540680 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 23.5135 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1432_length_42388_cov_13.459550 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1432_length_42388_cov_13.459550 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746217_bin.212 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia;s__Romboutsia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.1432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Clostridium phage phi8074-B1 virus enrichment approach none ERS11142647 SAMEA13540681 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.20800152472944827 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540681 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 18.9132 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_158_length_119469_cov_10.889356 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_158_length_119469_cov_10.889356 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.158 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142648 SAMEA13540682 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540682 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 12.646 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 110 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1805_length_37242_cov_7.219508 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1805_length_37242_cov_7.219508 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.33 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448;s__CAG-448 sp003150135 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.1805 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142649 SAMEA13540683 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.0490368859781216 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540683 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 8.63135 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 669 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1923_length_35937_cov_4.678277 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_1923_length_35937_cov_4.678277 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME283914 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900066565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.1923 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142650 SAMEA13540684 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746051. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540684 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 33.4045 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_213_length_105643_cov_19.626850 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7560975609756098 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_213_length_105643_cov_19.626850 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.213 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142651 SAMEA13540685 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746051. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540685 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.9004 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 126 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_233_length_103068_cov_6.644318 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7073170731707317 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_233_length_103068_cov_6.644318 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME101580 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster;s__Enterocloster sp000431375 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142652 SAMEA13540686 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746051. BACPHLIP temperate score 0.17747797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540686 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 28.9254 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_262_length_97696_cov_18.487292 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 21 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.9659090909090908 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_262_length_97696_cov_18.487292 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.262 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142653 SAMEA13540687 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.07725770925110134 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540687 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 685.836 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_3013_length_26772_cov_420.191834 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_3013_length_26772_cov_420.191834 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738661_virus.4060 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142654 SAMEA13540688 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746051. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540688 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 14.4375 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_34_length_203845_cov_8.262097 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_34_length_203845_cov_8.262097 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.34 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142655 SAMEA13540689 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7746051. BACPHLIP temperate score 0.556855397479522 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540689 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 11.3781 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_4134_length_21797_cov_6.999448 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_4134_length_21797_cov_6.999448 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0196334 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142656 SAMEA13540690 2100421 uncultured Caudovirales phage This sample represents an uncultured Gregsiragusavirus virus assembled from ERR7746051. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540690 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 18.8782 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_4927_length_19328_cov_10.788323 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_4927_length_19328_cov_10.788323 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.4927 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Guelinviridae; Denniswatsonvirinae; Gregsiragusavirus virus enrichment approach none ERS11142657 SAMEA13540691 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540691 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 47.7335 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 44 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_5654_length_17514_cov_29.006251 Viral contig found in MAG ERR7746051_bin.154 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_5654_length_17514_cov_29.006251 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.456 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142658 SAMEA13540692 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540692 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 17.6383 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 1128 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_745_length_60528_cov_10.663728 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6585365853658537 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_745_length_60528_cov_10.663728 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738621_virus.263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142659 SAMEA13540693 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746051. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540693 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 84.8302 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_813_length_58405_cov_50.065543 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_813_length_58405_cov_50.065543 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.813 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142660 SAMEA13540694 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746051. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540694 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 14.4217 MAG coverage software Reads (ERR7746051) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560669) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-E-H_A_21_1706__NODE_996_length_52263_cov_8.147568 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7241379310344828 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585949 sample name Hadza_MoBio_hadza-E-H_A_21_1706__NODE_996_length_52263_cov_8.147568 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME283914 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900066565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.996 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142661 SAMEA13540695 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746061. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540695 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 351.161 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 95 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1411_length_63916_cov_196.040352_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1411_length_63916_cov_196.040352_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_provirus.854 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142662 SAMEA13540696 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746061. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540696 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 43.1935 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 141 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2245_length_45695_cov_27.760796_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2245_length_45695_cov_27.760796_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0342275 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142663 SAMEA13540697 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746061. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540697 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 15.756 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_381_length_134143_cov_8.832306_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 11 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_381_length_134143_cov_8.832306_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746738_bin.136 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900554275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142664 SAMEA13540698 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746061. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540698 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 31.4116 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_59_length_304942_cov_17.682371_1 Viral contig found in MAG ERR7746061_bin.217 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_59_length_304942_cov_17.682371_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_provirus.59 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142665 SAMEA13540699 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746061. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540699 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 18.6676 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 134 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_917_length_83399_cov_10.625597_1 Viral contig found in MAG ERR7746061_bin.313 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_917_length_83399_cov_10.625597_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_provirus.917 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142666 SAMEA13540700 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746061. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540700 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 497.388 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 127 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1254_length_68759_cov_272.913806 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1254_length_68759_cov_272.913806 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.1254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142667 SAMEA13540701 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540701 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 22.1854 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 51 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1617_length_58504_cov_12.835333 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.32142857142857145 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1617_length_58504_cov_12.835333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_virus.440 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142668 SAMEA13540702 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540702 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 13.9181 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1893_length_52273_cov_7.539562 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_1893_length_52273_cov_7.539562 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME122359 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.1893 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142669 SAMEA13540703 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540703 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 136.612 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2221_length_46078_cov_74.803787 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6486486486486487 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2221_length_46078_cov_74.803787 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.2221 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142670 SAMEA13540704 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540704 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 100.896 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_235_length_170493_cov_57.235089 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 91.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_235_length_170493_cov_57.235089 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142671 SAMEA13540705 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540705 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 23.1729 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2623_length_40533_cov_13.144577 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.38461538461538464 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2623_length_40533_cov_13.144577 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.2623 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142672 SAMEA13540706 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540706 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 23.9042 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2741_length_39362_cov_13.460099 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_2741_length_39362_cov_13.460099 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746692_virus.650 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142673 SAMEA13540707 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540707 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 7.96144 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_3099_length_35655_cov_4.244533 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_3099_length_35655_cov_4.244533 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger variabilis_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738609_provirus.442 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142674 SAMEA13540708 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540708 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 21.9786 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_327_length_141992_cov_11.995483 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_327_length_141992_cov_11.995483 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.354 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745378_virus.122 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142675 SAMEA13540709 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540709 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:35Z INSDC last update 2022-12-27T01:22:35Z INSDC status public MAG coverage depth 17.6232 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 84 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_366_length_136311_cov_9.542273 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 25 number of unique standard tRNAs extracted 18 percent of BLAST hits supporting viral taxonomy 0.5974025974025974 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_366_length_136311_cov_9.542273 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380017 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142676 SAMEA13540710 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540710 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 126.516 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 159 Number of CRISPR spacer hits supporting host taxonomy 109 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_3877_length_29956_cov_71.077981 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_3877_length_29956_cov_71.077981 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738261_virus.503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142677 SAMEA13540711 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.07068695990175425 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540711 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 14.3547 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_4423_length_26948_cov_7.859737 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_4423_length_26948_cov_7.859737 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142678 SAMEA13540712 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.00135789431064384 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540712 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 8.10735 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_4920_length_24669_cov_4.221861 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_4920_length_24669_cov_4.221861 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746061_virus.4920 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142679 SAMEA13540713 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746061. BACPHLIP temperate score 0.939977973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540713 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 46.2915 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 116 Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_6145_length_20503_cov_25.678106 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_6145_length_20503_cov_25.678106 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745975_virus.2469 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142680 SAMEA13540714 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746061. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540714 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 12.4158 MAG coverage software Reads (ERR7746061) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560646) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_J_22_1662__NODE_7311_length_17753_cov_6.751358 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 53.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585905 sample name Hadza_MoBio_hadza-A-D_J_22_1662__NODE_7311_length_17753_cov_6.751358 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.4689 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142681 SAMEA13540715 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746094. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540715 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 32.9669 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_1156_length_68310_cov_19.176879_1 Viral contig found in MAG ERR7746094_bin.363 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_1156_length_68310_cov_19.176879_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME169940 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp003487665 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745648_provirus.969 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142682 SAMEA13540716 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746094. BACPHLIP temperate score 0.11433820478765556 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540716 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 28.3397 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2147_length_45059_cov_16.263216_1 Viral contig found in MAG ERR7746094_bin.174 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2147_length_45059_cov_16.263216_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_provirus.1261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142683 SAMEA13540717 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746094. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540717 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 17.2015 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_3762_length_28818_cov_9.760690_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_3762_length_28818_cov_9.760690_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738535_provirus.311 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142684 SAMEA13540718 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7746094. BACPHLIP temperate score 0.15590814195772124 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540718 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 64.1274 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_922_length_78267_cov_37.673360_1 Viral contig found in MAG ERR7746094_bin.148 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_922_length_78267_cov_37.673360_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_provirus.503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142685 SAMEA13540719 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746094. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540719 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 429.784 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_150_length_197298_cov_237.874020 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5121951219512195 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_150_length_197298_cov_237.874020 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024514 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372;s__UBA4372 sp900543815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_virus.70 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142686 SAMEA13540720 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746094. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540720 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 203.083 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_1933_length_48523_cov_116.085621 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4583333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_1933_length_48523_cov_116.085621 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.1933 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142687 SAMEA13540721 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746094. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13540721 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-28T19:46:23Z INSDC status public MAG coverage depth 33.1722 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2309_length_42949_cov_19.931960 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2309_length_42949_cov_19.931960 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_virus.746 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142688 SAMEA13540722 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746094. BACPHLIP temperate score 0.15927917672702033 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540722 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.74003 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2536_length_39682_cov_5.465547 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2536_length_39682_cov_5.465547 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128517 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900290275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.632 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142689 SAMEA13540723 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746094. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540723 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 30.0626 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2809_length_36642_cov_19.315876 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_2809_length_36642_cov_19.315876 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738616_provirus.420 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142690 SAMEA13540724 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746094. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540724 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 16.3733 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_3172_length_33331_cov_8.847477 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_3172_length_33331_cov_8.847477 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.3172 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142691 SAMEA13540725 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746094. BACPHLIP temperate score 0.28059885417488195 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540725 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 60.4946 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_3761_length_28819_cov_35.575569 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_3761_length_28819_cov_35.575569 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.2411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142692 SAMEA13540726 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746094. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540726 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 17.9936 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_4314_length_25534_cov_10.677142 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_4314_length_25534_cov_10.677142 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.1351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142693 SAMEA13540727 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746094. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540727 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 13.3252 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_4949_length_22644_cov_7.443967 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7222222222222222 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_4949_length_22644_cov_7.443967 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745346_bin.170 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900768995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.4949 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142694 SAMEA13540728 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746094. BACPHLIP temperate score 0.01358752575482346 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540728 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 42.4279 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_5674_length_19976_cov_24.244183 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_5674_length_19976_cov_24.244183 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745989_bin.40 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS2068;s__UMGS2068 sp900769635 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_virus.2492 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142695 SAMEA13540729 2100421 uncultured Caudovirales phage This sample represents an uncultured Beecentumtrevirus virus assembled from ERR7746094. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540729 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 45.5 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_7024_length_16361_cov_29.462601 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_7024_length_16361_cov_29.462601 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738569_virus.5962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae; Picovirinae; Beecentumtrevirus virus enrichment approach none ERS11142696 SAMEA13540730 1701671 uncultured podovirus This sample represents an uncultured Salmonella phage assan virus assembled from ERR7746094. BACPHLIP temperate score 0.14709484992950092 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540730 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 19.751 MAG coverage software Reads (ERR7746094) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561846) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_G_14_1102__NODE_9819_length_12000_cov_11.051172 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585526 sample name Hadza_MoBio_hadza-A-D_G_14_1102__NODE_9819_length_12000_cov_11.051172 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_virus.6216 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus; Salmonella phage assan virus enrichment approach none ERS11142697 SAMEA13540731 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746101. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540731 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.61888 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_176_length_128538_cov_5.181767_1 Viral contig found in MAG ERR7746101_bin.119 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_176_length_128538_cov_5.181767_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.1871 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142698 SAMEA13540732 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746101. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540732 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 74.5694 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_881_length_53354_cov_44.005837_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_881_length_53354_cov_44.005837_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_provirus.881 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142699 SAMEA13540733 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746101. BACPHLIP temperate score 0.08814699712046228 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540733 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.80322 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_1326_length_40865_cov_5.199544 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_1326_length_40865_cov_5.199544 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.2296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142700 SAMEA13540734 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746101. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540734 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 24.0273 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_1527_length_37075_cov_13.754176 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_1527_length_37075_cov_13.754176 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.82 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS874;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.1024 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142701 SAMEA13540735 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7746101. BACPHLIP temperate score 0.04117563148169571 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540735 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 20.464 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 396 Number of CRISPR spacer hits supporting host taxonomy 512 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_1789_length_33064_cov_11.694789 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_1789_length_33064_cov_11.694789 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11142702 SAMEA13540736 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746101. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540736 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 19.9995 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_214_length_118569_cov_11.127460 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.660377358490566 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_214_length_118569_cov_11.127460 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738174_bin.87 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1994;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.214 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142703 SAMEA13540737 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr130_1 virus assembled from ERR7746101. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540737 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 182.594 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_293_length_97742_cov_102.959863 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7628865979381443 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_293_length_97742_cov_102.959863 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268072 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella stercorea vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.211 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr130_1 virus enrichment approach none ERS11142704 SAMEA13540738 336724 Myoviridae environmental samples This sample represents an uncultured Takahashivirus virus assembled from ERR7746101. BACPHLIP temperate score 0.45 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540738 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 22.6919 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_46_length_227439_cov_12.970888 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_46_length_227439_cov_12.970888 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140265 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia;s__Blautia stercoris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.46 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Takahashivirus virus enrichment approach none ERS11142705 SAMEA13540739 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746101. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540739 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 111.532 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_66_length_197036_cov_62.405460 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 12 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_66_length_197036_cov_62.405460 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747083_bin.116 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1994;s__UMGS1994 sp900556975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.92 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142706 SAMEA13540740 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746101. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540740 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 26.3541 MAG coverage software Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-A-D_K_22_1166__NODE_822_length_55956_cov_14.714043 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585590 sample name Hadza_MoBio_hadza-A-D_K_22_1166__NODE_822_length_55956_cov_14.714043 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.1503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142707 SAMEA13540741 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746111. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540741 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 34.9715 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 161 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_1230_length_48969_cov_39.512476_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 73.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_1230_length_48969_cov_39.512476_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746785_virus.1002 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142708 SAMEA13540742 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746111. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540742 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 11.4171 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 97 Number of CRISPR spacer hits supporting host taxonomy 80 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_1825_length_37202_cov_6.690559_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_1825_length_37202_cov_6.690559_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_provirus.1825 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142709 SAMEA13540743 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7746111. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540743 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.46376 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 98 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_394_length_95096_cov_5.391269_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_394_length_95096_cov_5.391269_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_provirus.394 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142710 SAMEA13540744 1701671 uncultured podovirus This sample represents an uncultured Vibrio phage douglas 12A4 provirus assembled from ERR7746111. BACPHLIP temperate score 0.25495594713656383 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540744 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 45.7255 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_800_length_63883_cov_27.545137_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 59.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_800_length_63883_cov_27.545137_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738199_virus.179 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Vibrio phage douglas 12A4 virus enrichment approach none ERS11142711 SAMEA13540745 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746111. BACPHLIP temperate score 0.2557089863334722 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540745 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.12866 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_1274_length_47872_cov_5.520410 Viral contig found in MAG ERR7746111_bin.117 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 81.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_1274_length_47872_cov_5.520410 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_virus.1274 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142712 SAMEA13540746 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746111. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540746 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 28.0521 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 74 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_2100_length_33539_cov_16.624440 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_2100_length_33539_cov_16.624440 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.999 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142713 SAMEA13540747 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746111. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540747 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 81.2399 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_2843_length_26430_cov_48.693014 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 55.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_2843_length_26430_cov_48.693014 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738144_bin.24 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900767615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745867_virus.243 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142714 SAMEA13540748 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746111. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540748 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 56.1265 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_353_length_102335_cov_34.197921 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_353_length_102335_cov_34.197921 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7737964_bin.98 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;s__Phascolarctobacterium_A sp900551335 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738617_virus.256 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142715 SAMEA13540749 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746111. BACPHLIP temperate score 0.04377392670077858 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540749 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 59.5432 MAG coverage software Reads (ERR7746111) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559340) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_I_4_2616__NODE_832_length_62446_cov_33.851160 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9428571428571428 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586325 sample name Hadza_MoBio_hadza-I-L_I_4_2616__NODE_832_length_62446_cov_33.851160 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_virus.832 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142716 SAMEA13540750 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746113. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540750 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 14.673 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_153_length_191232_cov_8.216332_1 Viral contig found in MAG ERR7746113_bin.157 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_153_length_191232_cov_8.216332_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_provirus.153 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142717 SAMEA13540751 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746113. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540751 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 28.5951 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2376_length_38996_cov_16.227729_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2376_length_38996_cov_16.227729_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME023798 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900543155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_virus.754 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142718 SAMEA13540752 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746113. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540752 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 30.5451 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_440_length_117293_cov_17.742484_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_440_length_117293_cov_17.742484_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738223_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__V9D3004;s__V9D3004 sp002349525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738223_virus.1366 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142719 SAMEA13540753 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746113. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540753 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 26.4467 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_805_length_84123_cov_14.689967_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_805_length_84123_cov_14.689967_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738243_bin.62 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900551495 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.158 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142720 SAMEA13540754 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746113. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540754 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 20.3803 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1201_length_64560_cov_11.231332 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1201_length_64560_cov_11.231332 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738593_virus.686 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142721 SAMEA13540755 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746113. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540755 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 257.06 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1290_length_61177_cov_144.506252 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1290_length_61177_cov_144.506252 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747426_bin.316 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D succinifaciens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.1290 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142722 SAMEA13540756 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746113. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540756 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 49.9287 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1716_length_49416_cov_27.510022 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1716_length_49416_cov_27.510022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746285_bin.102 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFTH01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.866 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142723 SAMEA13540757 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746113. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540757 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 17.0786 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1988_length_44517_cov_9.374190 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6470588235294118 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_1988_length_44517_cov_9.374190 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_provirus.500 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142724 SAMEA13540758 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7746113. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540758 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 109.939 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 875 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2090_length_42872_cov_62.675757 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9032258064516128 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2090_length_42872_cov_62.675757 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738598_virus.929 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142725 SAMEA13540759 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7746113. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540759 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 15.1008 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 217 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2294_length_39984_cov_8.326284 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2294_length_39984_cov_8.326284 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.2294 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11142726 SAMEA13540760 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746113. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540760 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 14.7399 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 62 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2399_length_38703_cov_8.380650 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.89 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2399_length_38703_cov_8.380650 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.267 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142727 SAMEA13540761 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746113. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540761 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 11.6774 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2548_length_36789_cov_6.319351 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_2548_length_36789_cov_6.319351 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738611_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__Firm-11;s__Firm-11 sp004556545 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.2548 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142728 SAMEA13540762 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746113. BACPHLIP temperate score 7.8965839962564e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540762 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 89.7192 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_275_length_147450_cov_49.863197 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.639344262295082 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_275_length_147450_cov_49.863197 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.275 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142729 SAMEA13540763 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746113. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540763 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 138.305 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_3014_length_32212_cov_75.835631 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_3014_length_32212_cov_75.835631 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.3014 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142730 SAMEA13540764 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746113. BACPHLIP temperate score 0.06734581497797357 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540764 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 43.3564 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_3440_length_28841_cov_23.861702 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_3440_length_28841_cov_23.861702 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME246707 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__Phil1;s__Phil1 sp001940855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.3440 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142731 SAMEA13540765 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746113. BACPHLIP temperate score 0.04215678870616059 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540765 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.65334 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_4521_length_22832_cov_5.178994 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_4521_length_22832_cov_5.178994 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS902;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_provirus.394 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142732 SAMEA13540766 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746113. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540766 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 13.0867 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_504_length_109923_cov_7.057826 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.675 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_504_length_109923_cov_7.057826 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746113_virus.504 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142733 SAMEA13540767 2133760 Siphoviridae environmental samples This sample represents an uncultured Likavirus virus assembled from ERR7746113. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540767 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 14.8842 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_5659_length_18505_cov_8.328468 Viral contig found in MAG ERR7746113_bin.95 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.59 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_5659_length_18505_cov_8.328468 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0240719 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arquatrovirinae; Likavirus virus enrichment approach none ERS11142734 SAMEA13540768 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746113. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540768 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 19.7169 MAG coverage software Reads (ERR7746113) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561888) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_E_6_1152__NODE_709_length_91040_cov_10.555160 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5348837209302325 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585576 sample name Hadza_MoBio_hadza-A-D_E_6_1152__NODE_709_length_91040_cov_10.555160 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738584_virus.279 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142735 SAMEA13540769 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746144. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540769 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 35.7416 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 46 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_169_length_87237_cov_17.592634_1 Viral contig found in MAG ERR7746144_bin.152 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_169_length_87237_cov_17.592634_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_provirus.169 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142736 SAMEA13540770 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746144. BACPHLIP temperate score 0.20743392070484584 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540770 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 32.1313 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_496_length_50526_cov_15.808658_1 Viral contig found in MAG ERR7746144_bin.57 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_496_length_50526_cov_15.808658_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.2031 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142737 SAMEA13540771 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746144. BACPHLIP temperate score 0.1234392592042222 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540771 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.77208 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_1250_length_28656_cov_4.734070 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_1250_length_28656_cov_4.734070 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745823_bin.247 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp900539115 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1364 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142738 SAMEA13540772 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746144. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540772 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 21.1479 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 58 Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_2268_length_19371_cov_10.231678 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_2268_length_19371_cov_10.231678 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_virus.2268 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142739 SAMEA13540773 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746144. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540773 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 35.5429 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_397_length_57809_cov_17.252962 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_397_length_57809_cov_17.252962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_virus.397 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142740 SAMEA13540774 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746144. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540774 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 16.4239 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_563_length_46566_cov_7.833574 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_563_length_46566_cov_7.833574 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_virus.693 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142741 SAMEA13540775 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746144. BACPHLIP temperate score 0.1432089863334723 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540775 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 17.6871 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_672_length_42249_cov_9.058333 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_672_length_42249_cov_9.058333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745438_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142742 SAMEA13540776 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746144. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540776 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 72.7935 MAG coverage software Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_K_12_1914__NODE_91_length_109951_cov_37.629703 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6944444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586057 sample name Hadza_MoBio_hadza-E-H_K_12_1914__NODE_91_length_109951_cov_37.629703 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080666 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum;s__Agathobaculum butyriciproducens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_virus.91 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142743 SAMEA13540777 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746184. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540777 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 10.0644 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1397_length_46813_cov_5.958041_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1397_length_46813_cov_5.958041_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745890_bin.370 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__W2P13-069;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_provirus.1397 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142744 SAMEA13540778 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746184. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540778 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 144.868 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_257_length_110347_cov_88.110248_1 Viral contig found in MAG ERR7746184_bin.201 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_257_length_110347_cov_88.110248_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738566_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142745 SAMEA13540779 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746184. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540779 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 203.696 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_482_length_81263_cov_121.161875_1 Viral contig found in MAG ERR7746184_bin.11 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_482_length_81263_cov_121.161875_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_provirus.482 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142746 SAMEA13540780 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746184. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540780 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 21.1336 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1006_length_55801_cov_12.612142 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1006_length_55801_cov_12.612142 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738607_virus.1165 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142747 SAMEA13540781 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746184. BACPHLIP temperate score 0.1371696035242291 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540781 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.82224 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1204_length_50825_cov_5.804189 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1204_length_50825_cov_5.804189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0367890 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142748 SAMEA13540782 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746184. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540782 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 15.4455 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 100 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1707_length_41316_cov_9.230219 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1707_length_41316_cov_9.230219 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142749 SAMEA13540783 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746184. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540783 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 17.7546 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 109 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1964_length_37935_cov_10.728644 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_1964_length_37935_cov_10.728644 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.1964 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142750 SAMEA13540784 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746184. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540784 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 12.0318 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_2211_length_34760_cov_7.189315 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_2211_length_34760_cov_7.189315 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_virus.1556 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142751 SAMEA13540785 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746184. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540785 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.23238 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_2707_length_30243_cov_5.277829 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_2707_length_30243_cov_5.277829 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142752 SAMEA13540786 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746184. BACPHLIP temperate score 0.2432438154783468 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540786 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 9.71987 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 77 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_3305_length_26395_cov_5.792233 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_3305_length_26395_cov_5.792233 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738165_virus.1127 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142753 SAMEA13540787 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746184. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540787 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 8.56069 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_4088_length_22715_cov_4.835454 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_4088_length_22715_cov_4.835454 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.4088 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142754 SAMEA13540788 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7746184. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540788 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 7.41965 MAG coverage software Reads (ERR7746184) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561544) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_N_5_1522__NODE_7773_length_13697_cov_4.215051 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585777 sample name Hadza_MoBio_hadza-A-D_N_5_1522__NODE_7773_length_13697_cov_4.215051 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.4256 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11142755 SAMEA13540789 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746185. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540789 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 56.5069 MAG coverage software Reads (ERR7746185) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560394) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_C_10_1834__NODE_213_length_23153_cov_32.876885 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586030 sample name Hadza_MoBio_hadza-E-H_C_10_1834__NODE_213_length_23153_cov_32.876885 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095938 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745561_provirus.52 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142756 SAMEA13540790 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746217. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540790 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 94.859 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1507_length_56976_cov_56.146294_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 68.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8095238095238095 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1507_length_56976_cov_56.146294_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142757 SAMEA13540791 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746217. BACPHLIP temperate score 0.08836726143764287 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540791 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 10.0505 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 238 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_2063_length_46715_cov_5.782774_1 Viral contig found in MAG ERR7746217_bin.403 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_2063_length_46715_cov_5.782774_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME111561 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_provirus.2063 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142758 SAMEA13540792 926697 uncultured Microviridae This sample represents an uncultured Chimpanzee faeces associated microphage 2 provirus assembled from ERR7746217. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540792 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 49.4781 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_432_length_109477_cov_29.443026_1_1 Viral contig found in MAG ERR7746217_bin.284 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_432_length_109477_cov_29.443026_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_provirus.432 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Chimpanzee faeces associated microphage 2 virus enrichment approach none ERS11142759 SAMEA13540793 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746217. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540793 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 13.298400000000001 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_634_length_93599_cov_7.790434_1 Viral contig found in MAG ERR7746217_bin.371 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 85.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_634_length_93599_cov_7.790434_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_provirus.634 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142760 SAMEA13540794 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746217. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540794 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:34Z INSDC last update 2022-12-27T01:22:34Z INSDC status public MAG coverage depth 71.8556 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1038_length_72460_cov_43.937720 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1038_length_72460_cov_43.937720 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251925 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__RUG472;s__RUG472 sp900545265 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.1153 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142761 SAMEA13540795 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746217. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27T01:22:33Z ENA-LAST-UPDATE 2022-12-27T01:22:33Z External Id SAMEA13540795 INSDC center name Stanford University School of Medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 383.113 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1346_length_61387_cov_227.849666 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1346_length_61387_cov_227.849666 scientific_name uncultured Caudovirales phage sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746436_virus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales ERS11142762 SAMEA13540796 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746217. BACPHLIP temperate score 0.4772577092511012 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540796 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 11.3738 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1780_length_51287_cov_6.822554 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 73.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1780_length_51287_cov_6.822554 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.1780 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142763 SAMEA13540797 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746217. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540797 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 33.3824 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1986_length_47802_cov_32.893263 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.380952380952381 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_1986_length_47802_cov_32.893263 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.1986 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142764 SAMEA13540798 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746217. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540798 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 80.9102 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 98 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_2215_length_44442_cov_48.918517 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_2215_length_44442_cov_48.918517 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.878 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142765 SAMEA13540799 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746217. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540799 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 12.1863 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_2467_length_41267_cov_7.370187 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_2467_length_41267_cov_7.370187 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0288227 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142766 SAMEA13540800 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746217. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540800 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 11.4153 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_278_length_129195_cov_6.526216 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 71.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_278_length_129195_cov_6.526216 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.278 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142767 SAMEA13540801 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746217. BACPHLIP temperate score 0.7069113353173286 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540801 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 32.0019 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 125 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_3193_length_34229_cov_19.211671 Viral contig found in MAG ERR7746217_bin.257 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_3193_length_34229_cov_19.211671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142768 SAMEA13540802 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746217. BACPHLIP temperate score 0.00991189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540802 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 21.4189 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_3710_length_30369_cov_12.962168 Viral contig found in MAG ERR7746217_bin.338 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_3710_length_30369_cov_12.962168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745989_bin.108 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG806;s__RUG806 sp900313475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738186_provirus.420 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142769 SAMEA13540803 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746217. BACPHLIP temperate score 0.04719162995594713 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540803 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 9.3573 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 120 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_4829_length_24379_cov_5.450086 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_4829_length_24379_cov_5.450086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.4829 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142770 SAMEA13540804 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746217. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540804 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 10.4874 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_5580_length_21636_cov_6.123197 Viral contig found in MAG ERR7746217_bin.339 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_5580_length_21636_cov_6.123197 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.5580 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142771 SAMEA13540805 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr271_1 virus assembled from ERR7746217. BACPHLIP temperate score 0.10247797356828196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540805 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 29.8069 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_666_length_92099_cov_18.248441 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8387096774193549 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_666_length_92099_cov_18.248441 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.428 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr271_1 virus enrichment approach none ERS11142772 SAMEA13540806 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746217. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540806 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 11.2141 MAG coverage software Reads (ERR7746217) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567680) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_794_length_83447_cov_6.821674 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.5853658536585366 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_12_2317__NODE_794_length_83447_cov_6.821674 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME247421 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__UBA11524;s__UBA11524 sp000437595 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.145 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142773 SAMEA13540807 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746219. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540807 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 267.238 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 101 Number of CRISPR spacer hits supporting host taxonomy 76 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_120_length_175472_cov_278.517825_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_120_length_175472_cov_278.517825_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_provirus.120 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142774 SAMEA13540808 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746219. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540808 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 22.7742 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 37 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_289_length_126621_cov_12.826132_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_289_length_126621_cov_12.826132_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_provirus.223 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142775 SAMEA13540809 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746219. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540809 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 56.0062 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_787_length_77329_cov_31.531002_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_787_length_77329_cov_31.531002_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746051_virus.618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142777 SAMEA13540811 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746219. BACPHLIP temperate score 0.06486784140969162 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540811 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 63.7114 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_1633_length_49310_cov_35.523226 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_1633_length_49310_cov_35.523226 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_virus.1633 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142778 SAMEA13540812 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746219. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540812 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 33.4907 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_2118_length_40191_cov_18.940395 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_2118_length_40191_cov_18.940395 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738194_provirus.273 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142779 SAMEA13540813 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746219. BACPHLIP temperate score 0.14523598014784908 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540813 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 10.3365 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_2473_length_35642_cov_5.653255 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 56.19 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_2473_length_35642_cov_5.653255 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_virus.2473 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142780 SAMEA13540814 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746219. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540814 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 15.3513 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 103 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_3440_length_26468_cov_8.205184 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_3440_length_26468_cov_8.205184 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142781 SAMEA13540815 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746219. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540815 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 14.6703 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_5144_length_18083_cov_8.311230 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_5144_length_18083_cov_8.311230 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738660_bin.360 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.4652 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142782 SAMEA13540816 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746233. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540816 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 20.6891 MAG coverage software Reads (ERR7746233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 94 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_C-REDO_D_5_1545__NODE_133_length_80603_cov_12.338797_1 Viral contig found in MAG ERR7746233_bin.64 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_MoBio_C-REDO_D_5_1545__NODE_133_length_80603_cov_12.338797_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0329648 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142783 SAMEA13540817 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746233. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540817 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 20.8457 MAG coverage software Reads (ERR7746233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 109 Submitter Id Hadza_MoBio_C-REDO_D_5_1545__NODE_45_length_149483_cov_11.844149_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5172413793103449 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_MoBio_C-REDO_D_5_1545__NODE_45_length_149483_cov_11.844149_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_provirus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142784 SAMEA13540818 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746233. BACPHLIP temperate score 0.34245594713656385 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540818 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 12.0289 MAG coverage software Reads (ERR7746233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 136 Submitter Id Hadza_MoBio_C-REDO_D_5_1545__NODE_225_length_55639_cov_6.982128 Viral contig found in MAG ERR7746233_bin.33 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_MoBio_C-REDO_D_5_1545__NODE_225_length_55639_cov_6.982128 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142785 SAMEA13540819 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746233. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540819 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 13.046 MAG coverage software Reads (ERR7746233) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560872) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_C-REDO_D_5_1545__NODE_607_length_27646_cov_7.365483 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_MoBio_C-REDO_D_5_1545__NODE_607_length_27646_cov_7.365483 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_virus.694 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142786 SAMEA13540820 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746285. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540820 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 11.7958 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1334_length_44749_cov_7.307799_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1334_length_44749_cov_7.307799_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.1334 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142787 SAMEA13540821 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746285. BACPHLIP temperate score 0.37747797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540821 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 10.6119 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_211_length_132671_cov_6.333869_1 Viral contig found in MAG ERR7746285_bin.242 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_211_length_132671_cov_6.333869_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738152_provirus.2 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142788 SAMEA13540822 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746285. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540822 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 12.3722 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_526_length_80704_cov_7.464460_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_526_length_80704_cov_7.464460_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.526 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142789 SAMEA13540823 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746285. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540823 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 11.3628 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_822_length_60457_cov_6.801722_1 Viral contig found in MAG ERR7746285_bin.79 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.5 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_822_length_60457_cov_6.801722_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.822 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142790 SAMEA13540824 336724 Myoviridae environmental samples This sample represents an uncultured Pbunavirus virus assembled from ERR7746285. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540824 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 297.355 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1261_length_46259_cov_180.399355 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5294117647058824 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1261_length_46259_cov_180.399355 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.1261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Pbunavirus virus enrichment approach none ERS11142791 SAMEA13540825 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540825 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 136.657 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1415_length_43179_cov_82.053060 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.35294117647058826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1415_length_43179_cov_82.053060 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME254918 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFMI01;s__SFMI01 sp004556155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745919_virus.889 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142792 SAMEA13540826 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540826 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 11.4219 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 150 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1631_length_39187_cov_6.731629 Viral contig found in MAG ERR7746285_bin.79 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1631_length_39187_cov_6.731629 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738576_virus.1308 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142793 SAMEA13540827 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540827 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 64.8372 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1791_length_36659_cov_40.005303 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_1791_length_36659_cov_40.005303 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.1791 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142794 SAMEA13540828 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.6375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540828 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 46.9946 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_2188_length_32271_cov_28.322762 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_2188_length_32271_cov_28.322762 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738576_bin.85 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_provirus.4 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142795 SAMEA13540829 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540829 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 7.47136 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 94 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_2829_length_27036_cov_4.370155 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_2829_length_27036_cov_4.370155 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.1663 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142796 SAMEA13540830 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540830 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 13.9355 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_3856_length_21970_cov_8.391860 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9411764705882352 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_3856_length_21970_cov_8.391860 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145587 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A;s__Slackia_A isoflavoniconvertens vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.3856 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142797 SAMEA13540831 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540831 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 12.1348 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_558_length_78398_cov_7.334776 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7027027027027027 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_558_length_78398_cov_7.334776 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.558 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142798 SAMEA13540832 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746285. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540832 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 56.5361 MAG coverage software Reads (ERR7746285) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567854) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 100 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_811_length_60826_cov_36.278671 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585799 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_12_1545__NODE_811_length_60826_cov_36.278671 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_virus.811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142799 SAMEA13540833 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746321. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540833 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 97.2864 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1218_length_54656_cov_63.144415_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1218_length_54656_cov_63.144415_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738251_virus.875 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142800 SAMEA13540834 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746321. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540834 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 93.4978 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 79 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_170_length_152660_cov_50.486955_1 Viral contig found in MAG ERR7746321_bin.285 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.68 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_170_length_152660_cov_50.486955_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745963_bin.410 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp001916075 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_provirus.194 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142801 SAMEA13540835 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746321. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540835 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 54.8982 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 106 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_268_length_123485_cov_31.020177_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9107142857142856 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_268_length_123485_cov_31.020177_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_provirus.268 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142802 SAMEA13540836 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746321. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540836 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 31.2541 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_428_length_98461_cov_18.262248_1 Viral contig found in MAG ERR7746321_bin.278 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_428_length_98461_cov_18.262248_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_provirus.322 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142803 SAMEA13540837 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746321. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540837 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 9.64564 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_745_length_73408_cov_5.027642_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8148148148148148 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_745_length_73408_cov_5.027642_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142804 SAMEA13540838 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746321. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540838 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 19.8381 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1082_length_58649_cov_15.653555 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 51.45 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1082_length_58649_cov_15.653555 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745384_bin.138 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900553155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.1155 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142805 SAMEA13540839 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746321. BACPHLIP temperate score 0.275 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540839 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 21.2279 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1631_length_45844_cov_12.365482 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1631_length_45844_cov_12.365482 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.1553 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142806 SAMEA13540840 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746321. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540840 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 127.803 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2107 Number of CRISPR spacer hits supporting host taxonomy 45 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1842_length_42666_cov_79.857404 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_1842_length_42666_cov_79.857404 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738200_virus.670 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142807 SAMEA13540841 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7746321. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540841 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 43.6014 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_2281_length_36917_cov_24.069897 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9772727272727272 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_2281_length_36917_cov_24.069897 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738530_bin.33 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium sp900539945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.2281 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11142808 SAMEA13540842 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746321. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540842 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 13.4635 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_2793_length_32273_cov_7.776991 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.65 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_2793_length_32273_cov_7.776991 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.386 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142809 SAMEA13540843 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746321. BACPHLIP temperate score 0.6375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540843 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 6.92584 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_3603_length_27012_cov_3.650009 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_3603_length_27012_cov_3.650009 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738623_bin.166 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.1266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142810 SAMEA13540844 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746321. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540844 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 61.3217 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1194 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_535_length_86813_cov_34.356473 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_535_length_86813_cov_34.356473 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746321_virus.535 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142811 SAMEA13540845 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746321. BACPHLIP temperate score 0.6125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540845 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 379.346 MAG coverage software Reads (ERR7746321) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567810) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 62 Number of CRISPR spacer hits supporting host taxonomy 31 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_967_length_62528_cov_213.104738 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8260869565217391 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585894 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_16_1650__NODE_967_length_62528_cov_213.104738 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_provirus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142812 SAMEA13540846 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746344. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540846 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 62.1156 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_189_length_131458_cov_37.638563_1 Viral contig found in MAG ERR7746344_bin.18 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_189_length_131458_cov_37.638563_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-605;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_provirus.629 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142813 SAMEA13540847 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746344. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540847 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 45.6642 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 94 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_436_length_93910_cov_29.288694_1 Viral contig found in MAG ERR7746344_bin.227 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_436_length_93910_cov_29.288694_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745948_virus.945 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142814 SAMEA13540848 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis provirus assembled from ERR7746344. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540848 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 20.8319 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 90 Number of CRISPR spacer hits supporting host taxonomy 453 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_724_length_71810_cov_12.325527_1 Viral contig found in MAG ERR7746344_bin.190 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_724_length_71810_cov_12.325527_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745922_virus.337 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11142815 SAMEA13540849 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746344. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540849 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 8.2997 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_1129_length_55459_cov_4.792568 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.75 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_1129_length_55459_cov_4.792568 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746344_virus.1129 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142816 SAMEA13540850 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746344. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540850 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 37.7042 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 172 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_1648_length_42303_cov_21.992232 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; HMM-based (lower-bound) completeness score 81.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_1648_length_42303_cov_21.992232 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142817 SAMEA13540851 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu virus assembled from ERR7746344. BACPHLIP temperate score 0.19860955218654155 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540851 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 7.53551 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_2100_length_35376_cov_4.359104 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.84 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_2100_length_35376_cov_4.359104 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738662_virus.611 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11142818 SAMEA13540852 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746344. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540852 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 8.9822 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_2794_length_27906_cov_5.174710 Viral contig found in MAG ERR7746344_bin.158 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_2794_length_27906_cov_5.174710 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738209_bin.88 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-822;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746344_virus.2794 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142819 SAMEA13540853 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746344. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540853 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 309.846 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_359_length_103237_cov_182.623711 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 19 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.9178082191780822 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_359_length_103237_cov_182.623711 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0368853 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142820 SAMEA13540854 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr130_1 virus assembled from ERR7746344. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540854 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 813.48 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_430_length_94704_cov_475.891162 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7454545454545455 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_430_length_94704_cov_475.891162 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME268072 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella stercorea vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738566_virus.370 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr130_1 virus enrichment approach none ERS11142821 SAMEA13540855 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746344. BACPHLIP temperate score 0.01238986784140969 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540855 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:32Z INSDC last update 2022-12-27T01:22:32Z INSDC status public MAG coverage depth 58.2894 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_6329_length_13011_cov_35.297754 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_6329_length_13011_cov_35.297754 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.262 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900544405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745384_virus.4192 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142822 SAMEA13540856 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746344. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540856 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 114.307 MAG coverage software Reads (ERR7746344) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559424) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_O_20_2642__NODE_909_length_63167_cov_67.290236 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-20 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586346 sample name Hadza_MoBio_hadza-I-L_O_20_2642__NODE_909_length_63167_cov_67.290236 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745384_virus.591 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142823 SAMEA13540857 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746345. BACPHLIP temperate score 0.17431493571559326 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540857 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 12.0976 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1117_length_54467_cov_6.906251_1 Viral contig found in MAG ERR7746345_bin.220 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1117_length_54467_cov_6.906251_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.2393 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142824 SAMEA13540858 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746345. BACPHLIP temperate score 0.06396789356545554 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540858 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 16.5649 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_20_length_329360_cov_9.616403_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_20_length_329360_cov_9.616403_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_virus.1312 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142825 SAMEA13540859 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. provirus assembled from ERR7746345. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540859 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 57.9243 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_4052_length_21988_cov_34.433116_1_1 Viral contig found in MAG ERR7746345_bin.235 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_4052_length_21988_cov_34.433116_1_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_provirus.13346 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142826 SAMEA13540860 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746345. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540860 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 18.937 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 53 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_852_length_63823_cov_10.906347_1 Viral contig found in MAG ERR7746345_bin.7 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8064516129032258 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_852_length_63823_cov_10.906347_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019659 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.2792 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142827 SAMEA13540861 340016 uncultured virus This sample represents an uncultured Klebsiella phage P-K7R virus assembled from ERR7746345. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540861 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 474.464 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1208_length_51750_cov_271.664467 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6533333333333333 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1208_length_51750_cov_271.664467 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME239725 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola plebeius_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.1208 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Klebsiella phage P-K7R virus enrichment approach none ERS11142828 SAMEA13540862 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746345. BACPHLIP temperate score 0.3032310127651904 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540862 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 22.9752 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_141_length_158221_cov_13.111854 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5116279069767442 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_141_length_158221_cov_13.111854 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME260250 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp900759995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.154 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142829 SAMEA13540863 2100421 uncultured Caudovirales phage This sample represents an uncultured Vectrevirus virus assembled from ERR7746345. BACPHLIP temperate score 5.538234328848e-4 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540863 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 10.7988 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1533_length_44243_cov_6.122266 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8245614035087719 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1533_length_44243_cov_6.122266 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.2022 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae; Molineuxvirinae; Vectrevirus virus enrichment approach none ERS11142830 SAMEA13540864 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746345. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540864 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 8.01749 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 100 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1661_length_42106_cov_4.424017 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42105263157894735 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1661_length_42106_cov_4.424017 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.878 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142831 SAMEA13540865 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746345. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540865 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 8.39311 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1821_length_39381_cov_4.619199 Viral contig found in MAG ERR7746345_bin.282 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_1821_length_39381_cov_4.619199 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.1821 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142832 SAMEA13540866 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746345. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540866 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 32.0593 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_2034_length_36230_cov_18.653943 Viral contig found in MAG ERR7746345_bin.119 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_2034_length_36230_cov_18.653943 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.2034 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142833 SAMEA13540867 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746345. BACPHLIP temperate score 0.03997797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540867 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 8.68493 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_2595_length_30413_cov_4.780030 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_2595_length_30413_cov_4.780030 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746345_virus.2595 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142834 SAMEA13540868 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7746345. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540868 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 5.45158 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_32229_length_3764_cov_2.806075 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 67.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_32229_length_3764_cov_2.806075 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME157422 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Eremiobacterota;c__Xenobia;o__Xenobiales;f__Xenobiaceae;g__Bruticola;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738227_virus.13835 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11142835 SAMEA13540869 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746345. BACPHLIP temperate score 0.17129856875493005 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540869 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 7.93286 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_4560_length_20050_cov_4.341361 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_4560_length_20050_cov_4.341361 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738265_bin.79 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__Clostridium sp900540255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738659_virus.2586 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142836 SAMEA13540870 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746345. BACPHLIP temperate score 0.06414554127551365 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540870 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 301.062 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_745_length_68647_cov_172.360522 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 77.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_745_length_68647_cov_172.360522 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747782_bin.118 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D berlinense vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.756 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142837 SAMEA13540871 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746345. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540871 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 33.771 MAG coverage software Reads (ERR7746345) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560644) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 300 Submitter Id Hadza_MoBio_hadza-A-D_H_24_1651__NODE_937_length_60387_cov_19.578478 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7555555555555555 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585895 sample name Hadza_MoBio_hadza-A-D_H_24_1651__NODE_937_length_60387_cov_19.578478 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738251_virus.168 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142838 SAMEA13540872 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746349. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540872 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 339.819 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1108_length_70335_cov_212.828048_1 Viral contig found in MAG ERR7746349_bin.171 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1108_length_70335_cov_212.828048_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_provirus.37 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142839 SAMEA13540873 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746349. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540873 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 9.2389 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 332 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1694_length_54387_cov_5.617124_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1694_length_54387_cov_5.617124_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME080845 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella pectinovora vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738205_provirus.488 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142840 SAMEA13540874 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746349. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540874 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 37.3154 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 65 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_2903_length_38319_cov_24.730584_1 Viral contig found in MAG ERR7746349_bin.292 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_2903_length_38319_cov_24.730584_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_provirus.2903 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142841 SAMEA13540875 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746349. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540875 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 38.4562 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 86 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_4724_length_27806_cov_23.730210_1 Viral contig found in MAG ERR7746349_bin.470 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_4724_length_27806_cov_23.730210_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME125875 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFFH01;s__SFFH01 sp900542395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_provirus.4724 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142842 SAMEA13540876 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746349. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540876 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 120.897 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_913_length_77526_cov_76.244032_1 Viral contig found in MAG ERR7746349_bin.164 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 68.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_913_length_77526_cov_76.244032_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091228 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900549865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738612_provirus.660 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142843 SAMEA13540877 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746349. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540877 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 53.2034 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 219 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1258_length_65136_cov_32.547933 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5172413793103449 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1258_length_65136_cov_32.547933 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745582_virus.413 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142844 SAMEA13540878 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7746349. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540878 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 81.3022 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 348 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1661_length_55147_cov_49.428545 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.56 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_1661_length_55147_cov_49.428545 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.1661 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11142845 SAMEA13540879 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746349. BACPHLIP temperate score 0.05247797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540879 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 92.8926 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_195_length_156742_cov_56.263186 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6078431372549019 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_195_length_156742_cov_56.263186 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.195 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142846 SAMEA13540880 2100421 uncultured Caudovirales phage This sample represents an uncultured Aeromonas phage PZL-Ah8 virus assembled from ERR7746349. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540880 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 9.81003 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_2599_length_41336_cov_5.912989 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_2599_length_41336_cov_5.912989 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.2599 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae; Studiervirinae; unclassified Studiervirinae; Aeromonas phage PZL-Ah8 virus enrichment approach none ERS11142847 SAMEA13540881 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746349. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540881 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 16.7683 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_2916_length_38203_cov_10.212322 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_2916_length_38203_cov_10.212322 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745975_bin.324 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__UMGS124;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.1554 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142848 SAMEA13540882 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746349. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540882 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 10.6347 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_3124_length_36538_cov_6.488467 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_3124_length_36538_cov_6.488467 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_provirus.1272893 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142849 SAMEA13540883 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746349. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540883 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 27.8326 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_359_length_120565_cov_17.037016 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.918918918918919 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_359_length_120565_cov_17.037016 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.359 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142850 SAMEA13540884 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746349. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540884 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 12.4062 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_4103_length_30575_cov_7.658830 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (medium-confidence) completeness score 72.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_4103_length_30575_cov_7.658830 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.4103 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142851 SAMEA13540885 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit virus assembled from ERR7746349. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540885 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 12.5247 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_506_length_103001_cov_7.662877 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.6578947368421053 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_506_length_103001_cov_7.662877 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME147678 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_G vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738643_virus.497 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11142852 SAMEA13540886 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746349. BACPHLIP temperate score 0.3375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540886 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 64.0465 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_63_length_246263_cov_38.912838 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.7017543859649122 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_63_length_246263_cov_38.912838 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.63 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142853 SAMEA13540887 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746349. BACPHLIP temperate score 0.775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540887 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 9.78891 MAG coverage software Reads (ERR7746349) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568042) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 570 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_909_length_77837_cov_5.870293 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-27 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585730 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_2_1315__NODE_909_length_77837_cov_5.870293 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738162_virus.273 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142854 SAMEA13540888 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746365. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540888 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 27.6117 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 111 Number of CRISPR spacer hits supporting host taxonomy 54 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1070_length_62571_cov_15.617867_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1070_length_62571_cov_15.617867_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738265_virus.401 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142855 SAMEA13540889 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746365. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540889 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 17.4121 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1685_length_48891_cov_10.510325_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1685_length_48891_cov_10.510325_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_provirus.507 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142856 SAMEA13540890 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746365. BACPHLIP temperate score 0.10914096916299568 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540890 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 244.662 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 36 Number of CRISPR spacer hits supporting host taxonomy 152 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2181_length_41912_cov_145.968232_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2181_length_41912_cov_145.968232_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0283404 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142857 SAMEA13540891 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746365. BACPHLIP temperate score 0.6125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540891 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 64.1701 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 123 Number of CRISPR spacer hits supporting host taxonomy 62 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_30_length_304173_cov_52.689864_1 Viral contig found in MAG ERR7746365_bin.201 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.34782608695652173 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_30_length_304173_cov_52.689864_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_provirus.30 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142858 SAMEA13540892 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746365. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540892 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 10.1893 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 31 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_414_length_103377_cov_5.456544_1 Viral contig found in MAG ERR7746365_bin.173 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_414_length_103377_cov_5.456544_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738664_provirus.351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142859 SAMEA13540893 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746365. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540893 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 9.34035 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_710_length_77279_cov_4.994858_1 Viral contig found in MAG ERR7746365_bin.223 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_710_length_77279_cov_4.994858_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738574_bin.3 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Beduini;s__Beduini sp900550005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_provirus.710 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142860 SAMEA13540894 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746365. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540894 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 137.947 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1009_length_64375_cov_75.891319 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8125 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1009_length_64375_cov_75.891319 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.1009 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142861 SAMEA13540895 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746365. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540895 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 16.4976 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 353 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1258_length_57486_cov_9.336132 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1258_length_57486_cov_9.336132 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738575_bin.23 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-279;s__CAG-279 sp000437795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738234_virus.618 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142862 SAMEA13540896 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7746365. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540896 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 56.1045 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1527_length_52100_cov_31.182362 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1527_length_52100_cov_31.182362 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745425_virus.296 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11142863 SAMEA13540897 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746365. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540897 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 203.09 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 166 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1909_length_45569_cov_117.186824 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_1909_length_45569_cov_117.186824 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738212_provirus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142864 SAMEA13540898 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Toutatis virus assembled from ERR7746365. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540898 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 25.8038 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 71 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2155_length_42175_cov_15.135090 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7948717948717948 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2155_length_42175_cov_15.135090 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_virus.1312 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Toutatisvirus; Faecalibacterium virus Toutatis virus enrichment approach none ERS11142865 SAMEA13540899 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746365. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540899 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 34.8031 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 185 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2396_length_39374_cov_18.660279 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8529411764705882 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2396_length_39374_cov_18.660279 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140265 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia;s__Blautia stercoris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745582_virus.1002 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142866 SAMEA13540900 2133760 Siphoviridae environmental samples This sample represents an uncultured Vegasvirus virus assembled from ERR7746365. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540900 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 20.3586 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2733_length_36452_cov_10.903038 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2733_length_36452_cov_10.903038 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.2733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Gochnauervirinae; Vegasvirus virus enrichment approach none ERS11142867 SAMEA13540901 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746365. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540901 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 27.617 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2875_length_35320_cov_14.902278 Viral contig found in MAG ERR7746365_bin.2 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_2875_length_35320_cov_14.902278 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745975_bin.324 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__UMGS124;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.1554 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142868 SAMEA13540902 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona virus assembled from ERR7746365. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540902 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 45.4808 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 104 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_3831_length_28773_cov_24.804363 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7727272727272727 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_3831_length_28773_cov_24.804363 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_provirus.470 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11142869 SAMEA13540903 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7746365. BACPHLIP temperate score 0.00991189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540903 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 175.825 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_462_length_98060_cov_98.043130 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.922077922077922 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_462_length_98060_cov_98.043130 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11142870 SAMEA13540904 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746365. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540904 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 137.391 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_55_length_234872_cov_78.652126 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7931034482758621 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_55_length_234872_cov_78.652126 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738630_virus.112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142871 SAMEA13540905 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746365. BACPHLIP temperate score 0.04666904456842997 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540905 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 7.30781 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_7202_length_18041_cov_3.877199 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 80.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_7202_length_18041_cov_3.877199 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.7202 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142872 SAMEA13540906 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7746365. BACPHLIP temperate score 0.18368843659633977 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540906 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 382.605 MAG coverage software Reads (ERR7746365) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568022) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_9605_length_14370_cov_215.009935 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-04-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106184 sample name Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_9605_length_14370_cov_215.009935 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738191_virus.3624 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11142873 SAMEA13540907 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746398. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540907 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 8.24174 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 74 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1677_length_41181_cov_4.849455_1 Viral contig found in MAG ERR7746398_bin.123 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1677_length_41181_cov_4.849455_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746113_bin.330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745291_provirus.37 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142874 SAMEA13540908 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746398. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540908 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 82.4849 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 128 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_328_length_104510_cov_48.995863_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.46875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_328_length_104510_cov_48.995863_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738177_provirus.254 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142875 SAMEA13540909 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746398. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540909 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 23.9687 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_944_length_59662_cov_14.171872_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_944_length_59662_cov_14.171872_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745967_virus.496 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142876 SAMEA13540910 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746398. BACPHLIP temperate score 0.18243392070484585 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540910 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 15.4176 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1441_length_45440_cov_9.258823 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6341463414634146 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1441_length_45440_cov_9.258823 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7747782_bin.309 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus;s__Duodenibacillus sp900544255 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.1441 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142877 SAMEA13540911 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746398. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540911 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 22.4176 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1786_length_39413_cov_13.582520 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1786_length_39413_cov_13.582520 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.1786 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142878 SAMEA13540912 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746398. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540912 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 190.54 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1956_length_37124_cov_112.960888 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_1956_length_37124_cov_112.960888 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME079077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000434935 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738230_virus.458 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142879 SAMEA13540913 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7746398. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540913 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 8.23525 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 159 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_2769_length_28579_cov_4.762087 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_2769_length_28579_cov_4.762087 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME024263 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides sp900549585 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0328206 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11142880 SAMEA13540914 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7746398. BACPHLIP temperate score 0.03997797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540914 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 611.472 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_356_length_100633_cov_360.364901 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.927536231884058 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_356_length_100633_cov_360.364901 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.356 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11142881 SAMEA13540915 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746398. BACPHLIP temperate score 0.03588928786936091 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540915 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 6.47474 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_4801_length_18084_cov_3.697229 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_4801_length_18084_cov_3.697229 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000448 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;s__CAG-353 sp900066885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.4801 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142882 SAMEA13540916 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746398. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540916 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 61.0066 MAG coverage software Reads (ERR7746398) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559822) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 53 Submitter Id Hadza_MoBio_hadza-I-L_G_7_2399__NODE_738_length_68350_cov_36.387445 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586236 sample name Hadza_MoBio_hadza-I-L_G_7_2399__NODE_738_length_68350_cov_36.387445 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.738 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142883 SAMEA13540917 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746411. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540917 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 83.6298 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 84 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_130_length_235648_cov_49.642787_1 Viral contig found in MAG ERR7746411_bin.35 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_130_length_235648_cov_49.642787_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.51 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142884 SAMEA13540919 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Brigit provirus assembled from ERR7746411. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540919 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 56.4096 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_182_length_203798_cov_33.876355_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5121951219512195 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_182_length_203798_cov_33.876355_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.539 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus;s__Negativibacillus sp900547015 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.182 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Brigitvirus; Faecalibacterium virus Brigit virus enrichment approach none ERS11142885 SAMEA13540920 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona provirus assembled from ERR7746411. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540920 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 13.7886 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 245 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_2440_length_55703_cov_8.599971_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_2440_length_55703_cov_8.599971_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.1666 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11142886 SAMEA13540921 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746411. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540921 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 150.83 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 245 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3191_length_46011_cov_93.173575_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3191_length_46011_cov_93.173575_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_virus.1407 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142887 SAMEA13540922 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746411. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540922 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 23.2318 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_4748_length_35086_cov_13.897484_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.48 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_4748_length_35086_cov_13.897484_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359419 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142888 SAMEA13540923 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746411. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540923 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 21.399 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 102 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_714_length_107463_cov_13.056749_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6226415094339622 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_714_length_107463_cov_13.056749_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_provirus.714 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142889 SAMEA13540924 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746411. BACPHLIP temperate score 0.625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540924 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 11.5518 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 96 Number of CRISPR spacer hits supporting host taxonomy 80 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_983_length_91439_cov_6.626519_1 Viral contig found in MAG ERR7746411_bin.521 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_983_length_91439_cov_6.626519_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014819 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510;s__CAG-510 sp000434615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738594_virus.1978 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142890 SAMEA13540925 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540925 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 41.3923 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_11925_length_16513_cov_24.574653 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_11925_length_16513_cov_24.574653 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.4145 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11142891 SAMEA13540926 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.11941492641683568 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540926 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 98.0921 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_14274_length_14064_cov_57.544799 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_14274_length_14064_cov_57.544799 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.7389 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11142892 SAMEA13540927 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540927 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 58.7347 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 43 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_162_length_212516_cov_36.401240 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5409836065573771 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_162_length_212516_cov_36.401240 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.162 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142893 SAMEA13540928 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7746411. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540928 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 10.5038 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_1979_length_63398_cov_6.076910 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 74.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_1979_length_63398_cov_6.076910 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738214_virus.237 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11142894 SAMEA13540929 2133760 Siphoviridae environmental samples This sample represents an uncultured Lambdavirus virus assembled from ERR7746411. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540929 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 57.0245 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 285 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_2308_length_57707_cov_34.049193 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_2308_length_57707_cov_34.049193 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.2308 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lambdavirus virus enrichment approach none ERS11142895 SAMEA13540930 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746411. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540930 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 21.4334 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_256_length_177750_cov_12.692255 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 21 number of unique standard tRNAs extracted 18 percent of BLAST hits supporting viral taxonomy 0.5666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_256_length_177750_cov_12.692255 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.256 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142896 SAMEA13540931 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540931 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 181.414 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 91 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3008_length_48061_cov_123.616664 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5416666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3008_length_48061_cov_123.616664 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_virus.1324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142897 SAMEA13540932 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-28 External Id SAMEA13540932 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-28T19:46:24Z INSDC status public MAG coverage depth 19.0013 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3286_length_45152_cov_11.321597 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3286_length_45152_cov_11.321597 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3286 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142898 SAMEA13540933 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.08480176211453745 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540933 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 42.1666 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3667_length_41972_cov_25.061320 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5454545454545454 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3667_length_41972_cov_25.061320 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738588_bin.338 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71;s__UBA71 sp006954465 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3667 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142899 SAMEA13540934 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540934 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 10.2496 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3951_length_39972_cov_5.875473 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_3951_length_39972_cov_5.875473 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.3951 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142900 SAMEA13540935 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540935 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:31Z INSDC last update 2022-12-27T01:22:31Z INSDC status public MAG coverage depth 20.1246 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_4266_length_37960_cov_11.999155 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5945945945945946 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_4266_length_37960_cov_11.999155 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.4266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142901 SAMEA13540936 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7746411. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540936 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 14.3012 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 61 Number of CRISPR spacer hits supporting host taxonomy 557 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_4708_length_35274_cov_8.772736 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7906976744186046 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_4708_length_35274_cov_8.772736 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_virus.805 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11142902 SAMEA13540937 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746411. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540937 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 400.447 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_5612_length_31171_cov_238.480543 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_5612_length_31171_cov_238.480543 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME099131 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000435075 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_virus.1434 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142903 SAMEA13540938 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.11513032049760293 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540938 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 23.4514 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_6309_length_28306_cov_14.150873 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_6309_length_28306_cov_14.150873 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738188_virus.809 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142904 SAMEA13540939 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.2330383012181856 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540939 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 7.68737 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_7075_length_25624_cov_4.228363 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_7075_length_25624_cov_4.228363 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738624_bin.188 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__ISO4-G1;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.1988 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142905 SAMEA13540940 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746411. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540940 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 20.407 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 64 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_7942_length_23296_cov_12.133554 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_7942_length_23296_cov_12.133554 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME091217 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__UMGS973;s__UMGS973 sp900547295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738266_virus.1785 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142906 SAMEA13540941 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7746411. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540941 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 4.62107 MAG coverage software Reads (ERR7746411) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4568013) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 35 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_89716_length_2409_cov_2.404374 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585536 sample name Hadza_PheChl_Fiber-Hadza-Nepal_A_2_1112__NODE_89716_length_2409_cov_2.404374 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio;s__Anaerovibrio sp900548165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745545_virus.11888 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142907 SAMEA13540942 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746433. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540942 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 12.145 MAG coverage software Reads (ERR7746433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_L_18_2327__NODE_202_length_104068_cov_6.794578_1 Viral contig found in MAG ERR7746433_bin.68 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-13 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9767441860465116 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586197 sample name Hadza_MoBio_hadza-E-H_L_18_2327__NODE_202_length_104068_cov_6.794578_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746433_provirus.202 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142908 SAMEA13540943 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746433. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540943 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 38.998 MAG coverage software Reads (ERR7746433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 48 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_L_18_2327__NODE_434_length_72104_cov_21.983950_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-13 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5769230769230769 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586197 sample name Hadza_MoBio_hadza-E-H_L_18_2327__NODE_434_length_72104_cov_21.983950_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745329_provirus.82 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142909 SAMEA13540944 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746433. BACPHLIP temperate score 0.05743392070484582 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540944 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 50.4699 MAG coverage software Reads (ERR7746433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_L_18_2327__NODE_893_length_46023_cov_28.631611_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-13 completeness approach CheckV; AAI-based (high-confidence) completeness score 79.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586197 sample name Hadza_MoBio_hadza-E-H_L_18_2327__NODE_893_length_46023_cov_28.631611_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025761 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;s__Dialister sp000434475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_provirus.19 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142910 SAMEA13540945 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746433. BACPHLIP temperate score 0.06133297914365541 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540945 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 13.4365 MAG coverage software Reads (ERR7746433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_L_18_2327__NODE_1618_length_29002_cov_7.559343 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-13 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586197 sample name Hadza_MoBio_hadza-E-H_L_18_2327__NODE_1618_length_29002_cov_7.559343 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738536_bin.61 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;s__UBA1777 sp900546515 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738623_virus.2878 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142911 SAMEA13540946 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7746433. BACPHLIP temperate score 0.15446967015660706 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540946 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 52.2817 MAG coverage software Reads (ERR7746433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_L_18_2327__NODE_2204_length_22366_cov_29.321055 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-13 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586197 sample name Hadza_MoBio_hadza-E-H_L_18_2327__NODE_2204_length_22366_cov_29.321055 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745687_bin.245 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382;s__UBA6382 sp900557555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.2946 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142912 SAMEA13540947 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7746433. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540947 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 16.949 MAG coverage software Reads (ERR7746433) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559630) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 34 Number of CRISPR spacer hits supporting host taxonomy 125 Submitter Id Hadza_MoBio_hadza-E-H_L_18_2327__NODE_587_length_61075_cov_9.611413 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-13 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586197 sample name Hadza_MoBio_hadza-E-H_L_18_2327__NODE_587_length_61075_cov_9.611413 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270564 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738141_virus.327 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11142913 SAMEA13540948 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746436. BACPHLIP temperate score 0.07349942002795122 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540948 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 15.7445 MAG coverage software Reads (ERR7746436) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559800) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_G_5_2395__NODE_277_length_74068_cov_9.650728_1 Viral contig found in MAG ERR7746436_bin.122 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586235 sample name Hadza_MoBio_hadza-I-L_G_5_2395__NODE_277_length_74068_cov_9.650728_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747128_provirus.718 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142914 SAMEA13540949 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746436. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540949 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 29.4536 MAG coverage software Reads (ERR7746436) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559800) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 59 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-I-L_G_5_2395__NODE_850_length_37515_cov_17.889551_1 Viral contig found in MAG ERR7746436_bin.54 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (medium-confidence) completeness score 66.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586235 sample name Hadza_MoBio_hadza-I-L_G_5_2395__NODE_850_length_37515_cov_17.889551_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738224_virus.1626 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142915 SAMEA13540950 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746436. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540950 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 61.5252 MAG coverage software Reads (ERR7746436) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559800) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_G_5_2395__NODE_166_length_97310_cov_37.823249 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586235 sample name Hadza_MoBio_hadza-I-L_G_5_2395__NODE_166_length_97310_cov_37.823249 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_provirus.151 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142916 SAMEA13540951 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746436. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540951 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 17.9435 MAG coverage software Reads (ERR7746436) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559800) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-I-L_G_5_2395__NODE_288_length_72460_cov_10.815178 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.71875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586235 sample name Hadza_MoBio_hadza-I-L_G_5_2395__NODE_288_length_72460_cov_10.815178 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251925 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-138;g__RUG472;s__RUG472 sp900545265 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.1153 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142917 SAMEA13540952 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746436. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540952 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 30.4757 MAG coverage software Reads (ERR7746436) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559800) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_G_5_2395__NODE_489_length_52787_cov_18.406450 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586235 sample name Hadza_MoBio_hadza-I-L_G_5_2395__NODE_489_length_52787_cov_18.406450 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME011266 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1696;s__UMGS1696 sp900554225 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.799 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142918 SAMEA13540953 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746436. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540953 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 17.2675 MAG coverage software Reads (ERR7746436) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559800) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-I-L_G_5_2395__NODE_635_length_45165_cov_10.421664 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586235 sample name Hadza_MoBio_hadza-I-L_G_5_2395__NODE_635_length_45165_cov_10.421664 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738534_virus.1068 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142919 SAMEA13540954 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746436. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540954 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 29.6842 MAG coverage software Reads (ERR7746436) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559800) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-I-L_G_5_2395__NODE_757_length_40301_cov_18.019541 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-14 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586235 sample name Hadza_MoBio_hadza-I-L_G_5_2395__NODE_757_length_40301_cov_18.019541 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738205_virus.821 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142920 SAMEA13540955 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746440. BACPHLIP temperate score 0.15966643118087134 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540955 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 14.3332 MAG coverage software Reads (ERR7746440) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_L_8_2320__NODE_162_length_124872_cov_8.298305_1 Viral contig found in MAG ERR7746440_bin.198 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_MoBio_hadza-E-H_L_8_2320__NODE_162_length_124872_cov_8.298305_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737966_provirus.195 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142921 SAMEA13540956 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746440. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540956 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 21.3826 MAG coverage software Reads (ERR7746440) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_L_8_2320__NODE_752_length_50552_cov_12.820129_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_MoBio_hadza-E-H_L_8_2320__NODE_752_length_50552_cov_12.820129_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_provirus.242 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142922 SAMEA13540957 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746440. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540957 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 16.3197 MAG coverage software Reads (ERR7746440) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_L_8_2320__NODE_1641_length_29808_cov_9.426693 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_MoBio_hadza-E-H_L_8_2320__NODE_1641_length_29808_cov_9.426693 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738550_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus;s__Sodaliphilus sp004557565 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746440_virus.1641 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142923 SAMEA13540958 1701671 uncultured podovirus This sample represents an uncultured CrAss-like virus sp. virus assembled from ERR7746440. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540958 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 20.9706 MAG coverage software Reads (ERR7746440) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_L_8_2320__NODE_265_length_92480_cov_12.067963 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_MoBio_hadza-E-H_L_8_2320__NODE_265_length_92480_cov_12.067963 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; CrAss-like virus sp. virus enrichment approach none ERS11142924 SAMEA13540959 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7746440. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540959 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 116.67 MAG coverage software Reads (ERR7746440) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_L_8_2320__NODE_5979_length_10870_cov_71.705921 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 92.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_MoBio_hadza-E-H_L_8_2320__NODE_5979_length_10870_cov_71.705921 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745890_virus.12584 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11142925 SAMEA13540960 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7746465. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540960 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 8.15092 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 121 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_1300_length_38118_cov_4.660156_1 Viral contig found in MAG ERR7746465_bin.51 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_1300_length_38118_cov_4.660156_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.1837 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142926 SAMEA13540961 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746465. BACPHLIP temperate score 0.04801252640094042 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540961 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 319.817 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 169 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_303_length_89576_cov_224.140460_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_303_length_89576_cov_224.140460_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.2119 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142927 SAMEA13540962 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746465. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540962 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 27.1024 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_870_length_50513_cov_16.618150_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_870_length_50513_cov_16.618150_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745828_virus.992 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142928 SAMEA13540963 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746465. BACPHLIP temperate score 0.13363893334599836 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540963 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 9.22843 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_1235_length_39594_cov_5.170104 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_1235_length_39594_cov_5.170104 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747128_virus.831 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142929 SAMEA13540964 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746465. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540964 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 16.4861 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 56 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_1740_length_30595_cov_9.562553 Viral contig found in MAG ERR7746465_bin.69 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.77 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_1740_length_30595_cov_9.562553 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142930 SAMEA13540965 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746465. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540965 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 11.5284 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_251_length_96119_cov_6.604413 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6551724137931034 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_251_length_96119_cov_6.604413 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143713 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738186_virus.233 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142931 SAMEA13540966 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746465. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540966 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 10.7884 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 196 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_538_length_65307_cov_6.142250 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_538_length_65307_cov_6.142250 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.538 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11142932 SAMEA13540967 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746465. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540967 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 14.5729 MAG coverage software Reads (ERR7746465) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559825) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_I_15_2475__NODE_8467_length_7045_cov_8.961682 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586249 sample name Hadza_MoBio_hadza-I-L_I_15_2475__NODE_8467_length_7045_cov_8.961682 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746030_virus.7705 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142933 SAMEA13540968 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746660. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540968 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 8.82822 MAG coverage software Reads (ERR7746660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-A-D_N_1_1524__NODE_394_length_44893_cov_4.850098_1 Viral contig found in MAG ERR7746660_bin.68 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585779 sample name Hadza_MoBio_hadza-A-D_N_1_1524__NODE_394_length_44893_cov_4.850098_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270871 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628;s__CAG-628 sp000438415 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746660_provirus.394 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142934 SAMEA13540969 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr271_1 virus assembled from ERR7746660. BACPHLIP temperate score 0.10247797356828196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540969 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 53.5617 MAG coverage software Reads (ERR7746660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_N_1_1524__NODE_131_length_91734_cov_30.130988 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.873015873015873 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585779 sample name Hadza_MoBio_hadza-A-D_N_1_1524__NODE_131_length_91734_cov_30.130988 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738184_virus.90 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr271_1 virus enrichment approach none ERS11142935 SAMEA13540970 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746660. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540970 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 31.6606 MAG coverage software Reads (ERR7746660) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561498) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_N_1_1524__NODE_564_length_35869_cov_16.716138 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.42857142857142855 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585779 sample name Hadza_MoBio_hadza-A-D_N_1_1524__NODE_564_length_35869_cov_16.716138 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746660_virus.564 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142936 SAMEA13540971 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746688. BACPHLIP temperate score 0.11445538818076476 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540971 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 14.4799 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1354_length_68429_cov_10.443732_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5263157894736842 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1354_length_68429_cov_10.443732_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.1354 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142937 SAMEA13540972 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746688. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540972 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 24.4251 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1952_length_55276_cov_14.042102_1 Viral contig found in MAG ERR7746688_bin.419 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7307692307692307 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1952_length_55276_cov_14.042102_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0250744 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142938 SAMEA13540973 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746688. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540973 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 18.278 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2349_length_48946_cov_10.485584_1 Viral contig found in MAG ERR7746688_bin.276 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 60.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2349_length_48946_cov_10.485584_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745890_bin.370 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__W2P13-069;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.2151 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142939 SAMEA13540974 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus provirus assembled from ERR7746688. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540974 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 94.4789 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 107 Number of CRISPR spacer hits supporting host taxonomy 707 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_290_length_154564_cov_58.549671_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 75.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_290_length_154564_cov_58.549671_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.290 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142940 SAMEA13540975 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746688. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540975 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 55.919 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_40_length_334446_cov_32.154018_1 Viral contig found in MAG ERR7746688_bin.424 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 83.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_40_length_334446_cov_32.154018_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.40 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142941 SAMEA13540976 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746688. BACPHLIP temperate score 0.45 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540976 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 19.5042 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_540_length_113659_cov_11.282483_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_540_length_113659_cov_11.282483_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746111_virus.311 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142942 SAMEA13540977 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746688. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540977 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 18.2787 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_7260_length_22006_cov_10.665101_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_7260_length_22006_cov_10.665101_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_provirus.7260 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142943 SAMEA13540978 2133760 Siphoviridae environmental samples This sample represents an uncultured Andromedavirus virus assembled from ERR7746688. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540978 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 63.7408 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1034_length_80152_cov_37.253450 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8108108108108109 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1034_length_80152_cov_37.253450 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.1034 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Andromedavirus virus enrichment approach none ERS11142944 SAMEA13540979 340016 uncultured virus This sample represents an uncultured Bacteroides phage LoVEphage virus assembled from ERR7746688. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540979 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 12.5527 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1503_length_64098_cov_6.933959 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 75.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5384615384615384 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1503_length_64098_cov_6.933959 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.1503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Bacteroides phage LoVEphage virus enrichment approach none ERS11142945 SAMEA13540980 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540980 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 91.8946 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 39 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1678_length_60490_cov_52.028818 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_1678_length_60490_cov_52.028818 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME026639 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900548625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.919 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142946 SAMEA13540981 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7746688. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540981 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 45.2251 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_18025_length_10521_cov_26.015380 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_18025_length_10521_cov_26.015380 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME023798 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900543155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738260_virus.5572 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11142948 SAMEA13540983 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540983 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 85.1364 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 66 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2290_length_49777_cov_48.393239 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.78 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2290_length_49777_cov_48.393239 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738148_bin.20 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A;s__Selenomonas_A sp900769615 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1295 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142949 SAMEA13540984 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.8574339207048457 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540984 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 25.5015 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2534_length_46670_cov_14.390638 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 76.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2534_length_46670_cov_14.390638 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000967 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum;s__Anaerotignum faecicola vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0345130 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142950 SAMEA13540985 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540985 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 444.933 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 78 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2826_length_43612_cov_250.180085 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5652173913043478 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2826_length_43612_cov_250.180085 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745823_bin.49 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001;s__SFJ001 sp004555865 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_virus.928 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142951 SAMEA13540986 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540986 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 66.227 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 51 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_302_length_152663_cov_37.805264 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 13 number of unique standard tRNAs extracted 11 percent of BLAST hits supporting viral taxonomy 0.5873015873015873 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_302_length_152663_cov_37.805264 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738579_virus.137 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142952 SAMEA13540987 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540987 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 26.7512 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_3259_length_39477_cov_15.416751 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_3259_length_39477_cov_15.416751 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098330 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9502;s__UBA9502 sp003506385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.3259 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142953 SAMEA13540988 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540988 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 115.805 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_3455_length_37946_cov_67.595078 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_3455_length_37946_cov_67.595078 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME005405 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus infantis_I vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.3455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142954 SAMEA13540989 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.85 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540989 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 19.1597 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_3675_length_36445_cov_11.525022 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7419354838709677 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_3675_length_36445_cov_11.525022 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME103816 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;s__Dorea_A longicatena vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.3675 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142955 SAMEA13540990 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7746688. BACPHLIP temperate score 0.00743392070484581 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540990 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 123.788 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_38935_length_5253_cov_72.074189 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_38935_length_5253_cov_72.074189 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738588_bin.321 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger sp004555405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738158_virus.17872 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11142957 SAMEA13540992 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746688. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540992 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 64.2391 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_476_length_122037_cov_35.687693 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_476_length_122037_cov_35.687693 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.476 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142958 SAMEA13540993 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.2 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540993 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 12.7165 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_6003_length_25484_cov_6.923604 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_6003_length_25484_cov_6.923604 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME157782 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp900547745 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746365_virus.2065 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142959 SAMEA13540994 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540994 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 56.5438 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_6355_length_24388_cov_32.113817 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_6355_length_24388_cov_32.113817 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME095879 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus sp900543065 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.6355 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142960 SAMEA13540995 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540995 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 11.735900000000001 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 60 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_7581_length_21250_cov_6.520569 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_7581_length_21250_cov_6.520569 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.7581 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142961 SAMEA13540996 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746688. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540996 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 18.0115 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_905_length_86567_cov_10.103573 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_905_length_86567_cov_10.103573 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.905 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11142963 SAMEA13540998 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746692. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540998 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 11.3666 MAG coverage software Reads (ERR7746692) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561431) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_C-REDO_B_7_1518__NODE_784_length_35407_cov_6.353071_1 Viral contig found in MAG ERR7746692_bin.38 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.93 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_MoBio_C-REDO_B_7_1518__NODE_784_length_35407_cov_6.353071_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745433_virus.1725 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142964 SAMEA13540999 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746692. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540999 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 19.2825 MAG coverage software Reads (ERR7746692) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561431) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_C-REDO_B_7_1518__NODE_185_length_85703_cov_10.649102 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.717391304347826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_MoBio_C-REDO_B_7_1518__NODE_185_length_85703_cov_10.649102 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P;s__Clostridium_P ventriculi vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738245_virus.379 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142965 SAMEA13541000 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746692. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541000 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 25.9325 MAG coverage software Reads (ERR7746692) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561431) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_C-REDO_B_7_1518__NODE_42_length_181224_cov_14.845750 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 6 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.6216216216216216 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_MoBio_C-REDO_B_7_1518__NODE_42_length_181224_cov_14.845750 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746692_virus.42 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142966 SAMEA13541001 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746692. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541001 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 23.2575 MAG coverage software Reads (ERR7746692) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561431) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_C-REDO_B_7_1518__NODE_647_length_39480_cov_13.063828 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.868421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_MoBio_C-REDO_B_7_1518__NODE_647_length_39480_cov_13.063828 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745411_provirus.835 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142967 SAMEA13541002 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746721. BACPHLIP temperate score 0.10860324158549196 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541002 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 19.4374 MAG coverage software Reads (ERR7746721) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 66 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-A-D_F_7_1572__NODE_365_length_46376_cov_10.016696_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7916666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106181 sample name Hadza_MoBio_hadza-A-D_F_7_1572__NODE_365_length_46376_cov_10.016696_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746184_virus.2079 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142968 SAMEA13541003 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746721. BACPHLIP temperate score 0.08243392070484583 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541003 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 11.2617 MAG coverage software Reads (ERR7746721) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 85 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-A-D_F_7_1572__NODE_1044_length_26030_cov_5.169691 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106181 sample name Hadza_MoBio_hadza-A-D_F_7_1572__NODE_1044_length_26030_cov_5.169691 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738580_provirus.733 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142969 SAMEA13541004 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7746721. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541004 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 83.5836 MAG coverage software Reads (ERR7746721) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 137 Submitter Id Hadza_MoBio_hadza-A-D_F_7_1572__NODE_180_length_67606_cov_42.472168 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106181 sample name Hadza_MoBio_hadza-A-D_F_7_1572__NODE_180_length_67606_cov_42.472168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738244_provirus.56 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11142971 SAMEA13541006 926697 uncultured Microviridae This sample represents an uncultured Microvirus sp. virus assembled from ERR7746721. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541006 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 7.59039 MAG coverage software Reads (ERR7746721) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-A-D_F_7_1572__NODE_7865_length_6605_cov_3.508578 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106181 sample name Hadza_MoBio_hadza-A-D_F_7_1572__NODE_7865_length_6605_cov_3.508578 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746721_virus.7865 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microvirus sp. virus enrichment approach none ERS11142972 SAMEA13541007 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746738. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541007 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 72.8025 MAG coverage software Reads (ERR7746738) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561505) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-A-D_N_9_1519__NODE_69_length_172153_cov_41.672616_1 Viral contig found in MAG ERR7746738_bin.8 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 87.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585775 sample name Hadza_MoBio_hadza-A-D_N_9_1519__NODE_69_length_172153_cov_41.672616_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745835_virus.292 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142973 SAMEA13541008 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746738. BACPHLIP temperate score 0.16497797356828195 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541008 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 12.5379 MAG coverage software Reads (ERR7746738) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561505) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 56 Submitter Id Hadza_MoBio_hadza-A-D_N_9_1519__NODE_1611_length_20996_cov_6.949233 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585775 sample name Hadza_MoBio_hadza-A-D_N_9_1519__NODE_1611_length_20996_cov_6.949233 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.1518 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142974 SAMEA13541009 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746738. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541009 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 16.2895 MAG coverage software Reads (ERR7746738) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561505) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 208 Submitter Id Hadza_MoBio_hadza-A-D_N_9_1519__NODE_504_length_55111_cov_9.441999 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585775 sample name Hadza_MoBio_hadza-A-D_N_9_1519__NODE_504_length_55111_cov_9.441999 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_virus.268 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142975 SAMEA13541010 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746738. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541010 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 43.5938 MAG coverage software Reads (ERR7746738) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561505) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-A-D_N_9_1519__NODE_745_length_41047_cov_24.396363 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6538461538461539 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585775 sample name Hadza_MoBio_hadza-A-D_N_9_1519__NODE_745_length_41047_cov_24.396363 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME115165 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02;s__F23-B02 sp002472405 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746738_virus.745 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142977 SAMEA13541012 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746739. BACPHLIP temperate score 0.18992024567263308 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541012 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 24.0043 MAG coverage software Reads (ERR7746739) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561457) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_P_1_1512__NODE_1367_length_24811_cov_13.124768 Viral contig found in MAG ERR7746739_bin.71 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585768 sample name Hadza_MoBio_hadza-A-D_P_1_1512__NODE_1367_length_24811_cov_13.124768 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746030_bin.308 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1081;s__UBA1081 sp900543395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746739_virus.1367 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142978 SAMEA13541013 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746739. BACPHLIP temperate score 0.1625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541013 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 25.0576 MAG coverage software Reads (ERR7746739) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561457) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_P_1_1512__NODE_461_length_52461_cov_13.751069 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585768 sample name Hadza_MoBio_hadza-A-D_P_1_1512__NODE_461_length_52461_cov_13.751069 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746757_virus.850 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142979 SAMEA13541014 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746741. BACPHLIP temperate score 0.6625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541014 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 38.8292 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 135 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_10_length_343173_cov_22.539374_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7714285714285715 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_10_length_343173_cov_22.539374_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_provirus.501 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11142980 SAMEA13541015 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746741. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541015 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 12.6281 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 234 Number of CRISPR spacer hits supporting host taxonomy 309 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_358_length_81260_cov_6.992806_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 11 number of unique standard tRNAs extracted 10 percent of BLAST hits supporting viral taxonomy 0.7555555555555555 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_358_length_81260_cov_6.992806_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745544_provirus.252 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142981 SAMEA13541016 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7746741. BACPHLIP temperate score 0.19493392070484583 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541016 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 17.3266 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 16 Number of CRISPR spacer hits supporting host taxonomy 406 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_76_length_168089_cov_10.393496_1 Viral contig found in MAG ERR7746741_bin.126 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.95 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_76_length_168089_cov_10.393496_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11142982 SAMEA13541017 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746741. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541017 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 24.3511 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 339 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1054_length_45223_cov_13.611593 Viral contig found in MAG ERR7746741_bin.168 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1054_length_45223_cov_13.611593 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745947_virus.1976 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142983 SAMEA13541018 2133760 Siphoviridae environmental samples This sample represents an uncultured Parabacteroides phage PDS1 virus assembled from ERR7746741. BACPHLIP temperate score 0.4629947229551451 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541018 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 3286.77 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 169 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1178_length_42218_cov_1780.142711 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1178_length_42218_cov_1780.142711 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0280262 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Parabacteroides phage PDS1 virus enrichment approach none ERS11142984 SAMEA13541019 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746741. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541019 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 46.4787 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 566 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1259_length_40674_cov_52.829593 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.14 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1259_length_40674_cov_52.829593 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142986 SAMEA13541021 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746741. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541021 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 10.5467 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 84 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1539_length_35934_cov_5.861199 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1539_length_35934_cov_5.861199 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_C vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745854_virus.2645 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142987 SAMEA13541022 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746741. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541022 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 27.1556 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 41 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1814_length_31705_cov_15.800209 Viral contig found in MAG ERR7746741_bin.9 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6956521739130435 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1814_length_31705_cov_15.800209 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746365_bin.336 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA5884;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738534_virus.1900 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142988 SAMEA13541023 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746741. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541023 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 46.9539 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_2152_length_28033_cov_27.803441 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_2152_length_28033_cov_27.803441 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME019335 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900546535 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.1358 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142989 SAMEA13541024 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746741. BACPHLIP temperate score 0.7125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541024 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 184.402 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_272_length_94048_cov_102.421162 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.56 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_272_length_94048_cov_102.421162 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.95 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142990 SAMEA13541025 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746741. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541025 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 294.073 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_410_length_76576_cov_163.626505 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.44 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_410_length_76576_cov_163.626505 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.410 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142992 SAMEA13541027 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746741. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541027 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 76.5079 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 139 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_828_length_51865_cov_44.879142 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4838709677419355 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_828_length_51865_cov_44.879142 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738147_virus.298 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142993 SAMEA13541028 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746741. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541028 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 169.058 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_991_length_47148_cov_93.969259 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_991_length_47148_cov_93.969259 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746465_virus.878 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142994 SAMEA13541029 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746742. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541029 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 14.1431 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 21 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_494_length_56977_cov_7.809982_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_494_length_56977_cov_7.809982_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738577_virus.832 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142995 SAMEA13541030 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746742. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541030 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 19.8367 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_1135_length_33750_cov_11.056930 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_1135_length_33750_cov_11.056930 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746742_virus.1135 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142996 SAMEA13541031 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746742. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541031 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 37.7435 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_179_length_100662_cov_20.864483 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 21 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.9479166666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_179_length_100662_cov_20.864483 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746742_virus.179 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11142997 SAMEA13541032 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746742. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541032 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 303.628 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 239 Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_243_length_87714_cov_172.847439 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_243_length_87714_cov_172.847439 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746742_virus.243 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142998 SAMEA13541033 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746742. BACPHLIP temperate score 0.06822090574375078 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541033 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 23.2994 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_3361_length_15634_cov_11.529665 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_3361_length_15634_cov_11.529665 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746742_virus.3361 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143000 SAMEA13541035 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746742. BACPHLIP temperate score 0.9294333617490468 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541035 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 33.2191 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 96 Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_770_length_43332_cov_18.272570 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6764705882352942 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_770_length_43332_cov_18.272570 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746742_virus.770 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143001 SAMEA13541036 340016 uncultured virus This sample represents an uncultured Viruses virus assembled from ERR7746742. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541036 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 169.437 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 173 Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_844_length_40536_cov_94.559381 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_844_length_40536_cov_94.559381 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738626_virus.2057 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses virus enrichment approach none ERS11143002 SAMEA13541037 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746748. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541037 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 11.328 MAG coverage software Reads (ERR7746748) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_K_12_1156__NODE_190_length_130128_cov_6.437667_1 Viral contig found in MAG ERR7746748_bin.114 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585580 sample name Hadza_MoBio_hadza-A-D_K_12_1156__NODE_190_length_130128_cov_6.437667_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.1871 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143003 SAMEA13541038 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746748. BACPHLIP temperate score 0.8 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541038 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 85.4691 MAG coverage software Reads (ERR7746748) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 281 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_K_12_1156__NODE_636_length_69768_cov_52.982824_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585580 sample name Hadza_MoBio_hadza-A-D_K_12_1156__NODE_636_length_69768_cov_52.982824_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_virus.962 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143004 SAMEA13541039 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746748. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541039 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 15.9227 MAG coverage software Reads (ERR7746748) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 38 Submitter Id Hadza_MoBio_hadza-A-D_K_12_1156__NODE_1220_length_43164_cov_9.220206 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6190476190476191 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585580 sample name Hadza_MoBio_hadza-A-D_K_12_1156__NODE_1220_length_43164_cov_9.220206 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.1220 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143006 SAMEA13541041 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746748. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541041 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 25.9895 MAG coverage software Reads (ERR7746748) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_K_12_1156__NODE_215_length_123480_cov_15.263430 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 19 number of unique standard tRNAs extracted 16 percent of BLAST hits supporting viral taxonomy 0.5945945945945946 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585580 sample name Hadza_MoBio_hadza-A-D_K_12_1156__NODE_215_length_123480_cov_15.263430 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738253_virus.287 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143007 SAMEA13541042 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7746748. BACPHLIP temperate score 0.09801627478646756 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541042 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 251.914 MAG coverage software Reads (ERR7746748) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_K_12_1156__NODE_324_length_100132_cov_146.559462 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 7 number of unique standard tRNAs extracted 6 percent of BLAST hits supporting viral taxonomy 0.9090909090909092 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585580 sample name Hadza_MoBio_hadza-A-D_K_12_1156__NODE_324_length_100132_cov_146.559462 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11143008 SAMEA13541043 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746748. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541043 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 71.4217 MAG coverage software Reads (ERR7746748) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_12_1156__NODE_713_length_64459_cov_40.998478 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585580 sample name Hadza_MoBio_hadza-A-D_K_12_1156__NODE_713_length_64459_cov_40.998478 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745432_virus.483 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143009 SAMEA13541044 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746751. BACPHLIP temperate score 0.25 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541044 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 29.4368 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_20_length_301549_cov_17.927101_1 Viral contig found in MAG ERR7746751_bin.102 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; HMM-based (lower-bound) completeness score 64.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_20_length_301549_cov_17.927101_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738192_bin.62 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732;s__UBA9732 sp001940825 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_provirus.20 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143010 SAMEA13541045 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.15863157861825958 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541045 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 22.6998 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1063_length_53163_cov_13.426591 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1063_length_53163_cov_13.426591 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746349_virus.1755 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143011 SAMEA13541046 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541046 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 7.91056 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 183 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1215_length_48406_cov_4.634836 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1215_length_48406_cov_4.634836 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.1215 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143012 SAMEA13541047 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541047 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 14.3647 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1383_length_43653_cov_8.506196 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1383_length_43653_cov_8.506196 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.1383 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143013 SAMEA13541048 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541048 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 18.0493 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1563_length_39583_cov_11.016453 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7619047619047619 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1563_length_39583_cov_11.016453 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745963_bin.54 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFTH01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.1563 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143015 SAMEA13541050 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541050 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 1020.98 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 41 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1772_length_36238_cov_619.285252 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1772_length_36238_cov_619.285252 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME026639 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__CAG-170 sp900548625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.1772 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143016 SAMEA13541051 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.2678713013780906 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541051 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 11.7249 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_2265_length_29168_cov_7.020728 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_2265_length_29168_cov_7.020728 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738167_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__SFHK01;s__SFHK01 sp004556395 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738602_provirus.644 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143017 SAMEA13541052 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541052 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 7.02938 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_2902_length_23192_cov_4.036816 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_2902_length_23192_cov_4.036816 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745908_bin.146 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duodenibacillus;s__Duodenibacillus massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745870_virus.1535 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11143018 SAMEA13541053 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746751. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541053 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 190.357 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_423_length_93187_cov_110.823220 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9333333333333332 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_423_length_93187_cov_110.823220 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.182 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-698;g__CAG-698;s__CAG-698 sp000431235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143019 SAMEA13541054 1701671 uncultured podovirus This sample represents an uncultured Salmonella phage assan virus assembled from ERR7746751. BACPHLIP temperate score 0.18068787764054067 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541054 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 15.8315 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_5264_length_13215_cov_9.395951 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5714285714285714 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_5264_length_13215_cov_9.395951 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140296 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TF01-11;s__TF01-11 sp003529475 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.5264 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus; Salmonella phage assan virus enrichment approach none ERS11143021 SAMEA13541056 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.1375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541056 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 181.189 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_92_length_192685_cov_106.686493 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6785714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_92_length_192685_cov_106.686493 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME025676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177;s__CAG-177 sp003514385 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738532_virus.62 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143022 SAMEA13541057 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746757. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541057 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 33.1083 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_210_length_120312_cov_19.034740_1 Viral contig found in MAG ERR7746757_bin.41 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.8076923076923077 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_210_length_120312_cov_19.034740_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738598_bin.181 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492;s__CAG-492 sp900557045 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746757_provirus.210 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143023 SAMEA13541058 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746757. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541058 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 128.242 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 82 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_552_length_68377_cov_89.201523_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_552_length_68377_cov_89.201523_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME033251 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella hominis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1726542 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143024 SAMEA13541059 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746757. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541059 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 37.2759 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 310 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_1132_length_43374_cov_23.459339 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_1132_length_43374_cov_23.459339 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738243_virus.814 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143025 SAMEA13541060 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746757. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541060 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 27.6772 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_1436_length_35663_cov_16.468246 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.42 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_1436_length_35663_cov_16.468246 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.2855 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11143026 SAMEA13541061 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746757. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541061 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 7.23602 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 105 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_1830_length_29364_cov_4.092840 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.47 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_1830_length_29364_cov_4.092840 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0272453 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143027 SAMEA13541062 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746757. BACPHLIP temperate score 0.15446967015660706 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541062 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 50.1175 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_2398_length_23650_cov_30.106775 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (medium-confidence) completeness score 82.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_2398_length_23650_cov_30.106775 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0203435 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143029 SAMEA13541064 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr131_1 virus assembled from ERR7746757. BACPHLIP temperate score 0.04741189427312775 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541064 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 9.05313 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_690_length_60233_cov_5.390834 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_690_length_60233_cov_5.390834 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME014888 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745588_virus.330 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr131_1 virus enrichment approach none ERS11143030 SAMEA13541065 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746757. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541065 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 38.2765 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_97_length_183948_cov_22.538160 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.07 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.987012987012987 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_97_length_183948_cov_22.538160 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738536_bin.336 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter;s__Terrisporobacter sp900557165 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746757_virus.97 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143031 SAMEA13541066 336724 Myoviridae environmental samples This sample represents an uncultured Tetrasphaera virus TJE1 provirus assembled from ERR7746767. BACPHLIP temperate score 0.1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541066 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 36.7025 MAG coverage software Reads (ERR7746767) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_H_10_2273__NODE_36_length_203734_cov_22.490928_1 Viral contig found in MAG ERR7746767_bin.61 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.2 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.64 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_MoBio_hadza-E-H_H_10_2273__NODE_36_length_203734_cov_22.490928_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_provirus.36 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tijeunavirus; Tetrasphaera virus TJE1 virus enrichment approach none ERS11143032 SAMEA13541067 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746767. BACPHLIP temperate score 0.8819113353173286 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541067 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 17.1534 MAG coverage software Reads (ERR7746767) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 389 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_H_10_2273__NODE_850_length_52203_cov_9.744600_1 Viral contig found in MAG ERR7746767_bin.10 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_MoBio_hadza-E-H_H_10_2273__NODE_850_length_52203_cov_9.744600_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746094_virus.2712 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143033 SAMEA13541068 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746767. BACPHLIP temperate score 0.12747797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541068 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 14.586 MAG coverage software Reads (ERR7746767) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 38 Number of CRISPR spacer hits supporting host taxonomy 536 Submitter Id Hadza_MoBio_hadza-E-H_H_10_2273__NODE_1460_length_38221_cov_8.614042 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6428571428571429 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_MoBio_hadza-E-H_H_10_2273__NODE_1460_length_38221_cov_8.614042 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_provirus.883 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143035 SAMEA13541070 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746767. BACPHLIP temperate score 0.075 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541070 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 7.9722 MAG coverage software Reads (ERR7746767) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 306 Submitter Id Hadza_MoBio_hadza-E-H_H_10_2273__NODE_2370_length_28061_cov_4.390294 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 78.02 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_MoBio_hadza-E-H_H_10_2273__NODE_2370_length_28061_cov_4.390294 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.865 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143036 SAMEA13541071 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746767. BACPHLIP temperate score 0.8625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541071 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 27.4017 MAG coverage software Reads (ERR7746767) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-E-H_H_10_2273__NODE_755_length_55524_cov_15.334734 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9767441860465116 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_MoBio_hadza-E-H_H_10_2273__NODE_755_length_55524_cov_15.334734 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.755 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143037 SAMEA13541072 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746768. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541072 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 409.151 MAG coverage software Reads (ERR7746768) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 116 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-I-L_L_5_1268__NODE_133_length_88816_cov_231.634422_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585686 sample name Hadza_MoBio_hadza-I-L_L_5_1268__NODE_133_length_88816_cov_231.634422_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME212098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746768_provirus.133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143038 SAMEA13541073 2133760 Siphoviridae environmental samples This sample represents an uncultured Bifidobacterium phage Bbif-1 virus assembled from ERR7746768. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541073 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 488.048 MAG coverage software Reads (ERR7746768) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561218) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 204 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_MoBio_hadza-I-L_L_5_1268__NODE_293_length_41986_cov_281.858622 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585686 sample name Hadza_MoBio_hadza-I-L_L_5_1268__NODE_293_length_41986_cov_281.858622 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745621_virus.292 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Bifidobacterium phage Bbif-1 virus enrichment approach none ERS11143039 SAMEA13541074 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746773. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541074 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 10.0694 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 76 Number of CRISPR spacer hits supporting host taxonomy 1089 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_1396_length_35033_cov_5.635771_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4583333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_1396_length_35033_cov_5.635771_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0362748 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143040 SAMEA13541075 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746773. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541075 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 10.2515 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 248 Number of CRISPR spacer hits supporting host taxonomy 133 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_513_length_68268_cov_5.748706_1 Viral contig found in MAG ERR7746773_bin.188 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6071428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_513_length_68268_cov_5.748706_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_provirus.513 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143041 SAMEA13541076 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746773. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541076 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 24.9409 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_1151_length_40554_cov_13.960941 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (medium-confidence) completeness score 65.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_1151_length_40554_cov_13.960941 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.708 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143042 SAMEA13541077 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746773. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541077 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 75.8453 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 177 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_1375_length_35490_cov_42.305735 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.85 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_1375_length_35490_cov_42.305735 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746285_provirus.191 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143044 SAMEA13541079 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746773. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541079 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 32.1614 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 486 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_3360_length_17034_cov_18.506752 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_3360_length_17034_cov_18.506752 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746144_virus.688 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143045 SAMEA13541080 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7746773. BACPHLIP temperate score 0.6954286436599909 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541080 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 22.5192 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 5 Number of CRISPR spacer hits supporting host taxonomy 60 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_574_length_63785_cov_12.839251 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_574_length_63785_cov_12.839251 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738273_virus.972 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11143046 SAMEA13541081 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7746773. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541081 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 35.401 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_80_length_173936_cov_19.957466 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 22 number of unique standard tRNAs extracted 18 percent of BLAST hits supporting viral taxonomy 0.6101694915254238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_80_length_173936_cov_19.957466 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746411_virus.256 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11143047 SAMEA13541082 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7746779. BACPHLIP temperate score 0.7375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541082 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 11.2237 MAG coverage software Reads (ERR7746779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 90 Submitter Id Hadza_MoBio_hadza-I-L_K_1_2479__NODE_1465_length_39255_cov_6.913089_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586253 sample name Hadza_MoBio_hadza-I-L_K_1_2479__NODE_1465_length_39255_cov_6.913089_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0345548 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143048 SAMEA13541083 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7746779. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541083 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 14.7506 MAG coverage software Reads (ERR7746779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 111 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-I-L_K_1_2479__NODE_338_length_99082_cov_8.478047_1 Viral contig found in MAG ERR7746779_bin.50 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7692307692307693 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586253 sample name Hadza_MoBio_hadza-I-L_K_1_2479__NODE_338_length_99082_cov_8.478047_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME107760 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000434975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.1837 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11143050 SAMEA13541085 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746779. BACPHLIP temperate score 0.7875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541085 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 25.6768 MAG coverage software Reads (ERR7746779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 544 Submitter Id Hadza_MoBio_hadza-I-L_K_1_2479__NODE_1330_length_42056_cov_21.235308 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5789473684210527 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586253 sample name Hadza_MoBio_hadza-I-L_K_1_2479__NODE_1330_length_42056_cov_21.235308 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745383_virus.314 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143051 SAMEA13541086 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746779. BACPHLIP temperate score 0.11227973568281942 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541086 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 7.1378 MAG coverage software Reads (ERR7746779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_K_1_2479__NODE_2536_length_23988_cov_3.866087 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586253 sample name Hadza_MoBio_hadza-I-L_K_1_2479__NODE_2536_length_23988_cov_3.866087 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_virus.1319 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143052 SAMEA13541087 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746779. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541087 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 12.6828 MAG coverage software Reads (ERR7746779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 33 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-I-L_K_1_2479__NODE_480_length_82966_cov_7.354522 Viral contig found in MAG ERR7746779_bin.26 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 79.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.48 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586253 sample name Hadza_MoBio_hadza-I-L_K_1_2479__NODE_480_length_82966_cov_7.354522 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738566_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745831_provirus.9 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143053 SAMEA13541088 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746785. BACPHLIP temperate score 0.20600085628426487 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541088 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 57.1279 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 104 Number of CRISPR spacer hits supporting host taxonomy 40 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_1170_length_45040_cov_34.834842_1 Viral contig found in MAG ERR7746785_bin.47 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 67.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9523809523809524 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_1170_length_45040_cov_34.834842_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME252988 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp900314705 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746785_provirus.1170 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143054 SAMEA13541089 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus provirus assembled from ERR7746785. BACPHLIP temperate score 0.225 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541089 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 72.632 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_357_length_90052_cov_41.632276_1 Viral contig found in MAG ERR7746785_bin.168 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.717948717948718 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_357_length_90052_cov_41.632276_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738176_provirus.230 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11143055 SAMEA13541090 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746785. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541090 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 51.8705 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_948_length_51298_cov_31.329767_1 Viral contig found in MAG ERR7746785_bin.92 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 82.6 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9473684210526316 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_948_length_51298_cov_31.329767_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME270871 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628;s__CAG-628 sp000438415 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746660_provirus.394 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143056 SAMEA13541091 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7746785. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541091 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 29.1266 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 370 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_132_length_142112_cov_17.283261 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.6136363636363636 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_132_length_142112_cov_17.283261 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001115 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium prausnitzii_E vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746785_virus.132 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11143058 SAMEA13541093 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746785. BACPHLIP temperate score 0.08942731277533046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541093 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 10.9883 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_2070_length_31484_cov_6.409940 Viral contig found in MAG ERR7746785_bin.286 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 85.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_2070_length_31484_cov_6.409940 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746785_virus.2070 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143059 SAMEA13541094 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746785. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541094 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 24.5496 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_3102_length_23409_cov_14.291788 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 58.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7777777777777778 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_3102_length_23409_cov_14.291788 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746111_bin.22 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251295 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737954_provirus.190 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143060 SAMEA13541095 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746785. BACPHLIP temperate score 0.03977380510648237 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541095 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 8.77109 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_4089_length_18725_cov_5.214768 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 54.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_4089_length_18725_cov_5.214768 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.3018 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143061 SAMEA13541096 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746785. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541096 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 10.4279 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 772 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_788_length_56865_cov_6.109618 Viral contig found in MAG ERR7746785_bin.285 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.64 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 4 number of unique standard tRNAs extracted 4 percent of BLAST hits supporting viral taxonomy 0.4516129032258064 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_788_length_56865_cov_6.109618 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746785_virus.788 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143062 SAMEA13541097 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746793. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541097 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 13.7371 MAG coverage software Reads (ERR7746793) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 47 Submitter Id Hadza_MoBio_hadza-A-D_D_17_1579__NODE_730_length_47772_cov_8.448013_1 Viral contig found in MAG ERR7746793_bin.23 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 82.01 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585828 sample name Hadza_MoBio_hadza-A-D_D_17_1579__NODE_730_length_47772_cov_8.448013_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746739_provirus.59 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143064 SAMEA13541099 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746793. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541099 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 114.123 MAG coverage software Reads (ERR7746793) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 211 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-A-D_D_17_1579__NODE_361_length_76740_cov_69.469614 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.36 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585828 sample name Hadza_MoBio_hadza-A-D_D_17_1579__NODE_361_length_76740_cov_69.469614 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128517 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900290275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.361 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143065 SAMEA13541100 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746793. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541100 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 18.8399 MAG coverage software Reads (ERR7746793) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_D_17_1579__NODE_768_length_46379_cov_11.585072 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585828 sample name Hadza_MoBio_hadza-A-D_D_17_1579__NODE_768_length_46379_cov_11.585072 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745994_bin.11 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.768 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143066 SAMEA13541101 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746794. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541101 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 49.3409 MAG coverage software Reads (ERR7746794) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561252) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 46 Submitter Id Hadza_MoBio_hadza-I-L_L_13_1278__NODE_152_length_88220_cov_28.290528_1 Viral contig found in MAG ERR7746794_bin.48 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585695 sample name Hadza_MoBio_hadza-I-L_L_13_1278__NODE_152_length_88220_cov_28.290528_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746794_provirus.152 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143067 SAMEA13541102 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746794. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541102 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 273.356 MAG coverage software Reads (ERR7746794) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561252) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 88 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-I-L_L_13_1278__NODE_37_length_190686_cov_152.821567_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585695 sample name Hadza_MoBio_hadza-I-L_L_13_1278__NODE_37_length_190686_cov_152.821567_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746794_provirus.37 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143068 SAMEA13541103 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746794. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541103 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 59.3649 MAG coverage software Reads (ERR7746794) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561252) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 44 Submitter Id Hadza_MoBio_hadza-I-L_L_13_1278__NODE_495_length_40468_cov_34.565076 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9803921568627452 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585695 sample name Hadza_MoBio_hadza-I-L_L_13_1278__NODE_495_length_40468_cov_34.565076 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745561_bin.8 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746794_virus.495 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143069 SAMEA13541104 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746794. BACPHLIP temperate score 0.1611458605941019 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541104 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 15.2967 MAG coverage software Reads (ERR7746794) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561252) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 19 Submitter Id Hadza_MoBio_hadza-I-L_L_13_1278__NODE_789_length_28349_cov_8.650538 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 64.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585695 sample name Hadza_MoBio_hadza-I-L_L_13_1278__NODE_789_length_28349_cov_8.650538 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME212098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus lutetiensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746794_virus.789 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143070 SAMEA13541105 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747083. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541105 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 32.916 MAG coverage software Reads (ERR7747083) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 58 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-A-D_F_17_1567__NODE_177_length_138215_cov_19.959504_1 Viral contig found in MAG ERR7747083_bin.140 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585821 sample name Hadza_MoBio_hadza-A-D_F_17_1567__NODE_177_length_138215_cov_19.959504_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745556_provirus.188 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143071 SAMEA13541106 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747083. BACPHLIP temperate score 0.3625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541106 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 37.4467 MAG coverage software Reads (ERR7747083) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Hadza_MoBio_hadza-A-D_F_17_1567__NODE_812_length_59303_cov_22.599821_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7096774193548387 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585821 sample name Hadza_MoBio_hadza-A-D_F_17_1567__NODE_812_length_59303_cov_22.599821_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738600_virus.1151 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143073 SAMEA13541108 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747083. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541108 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 56.3894 MAG coverage software Reads (ERR7747083) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_F_17_1567__NODE_1831_length_33290_cov_32.906362 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585821 sample name Hadza_MoBio_hadza-A-D_F_17_1567__NODE_1831_length_33290_cov_32.906362 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738557_bin.224 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__Ruminococcus sp900540005 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738278_virus.840 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143074 SAMEA13541109 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747083. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541109 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 35.4683 MAG coverage software Reads (ERR7747083) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_F_17_1567__NODE_2757_length_24007_cov_20.980025 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (medium-confidence) completeness score 67.4 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585821 sample name Hadza_MoBio_hadza-A-D_F_17_1567__NODE_2757_length_24007_cov_20.980025 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738544_provirus.1098 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143075 SAMEA13541110 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7747083. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541110 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 18.2589 MAG coverage software Reads (ERR7747083) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_F_17_1567__NODE_411_length_91184_cov_10.693898 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7435897435897436 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585821 sample name Hadza_MoBio_hadza-A-D_F_17_1567__NODE_411_length_91184_cov_10.693898 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747083_virus.411 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11143076 SAMEA13541111 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7747083. BACPHLIP temperate score 0.6729066172282728 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541111 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 256.783 MAG coverage software Reads (ERR7747083) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 83 Submitter Id Hadza_MoBio_hadza-A-D_F_17_1567__NODE_791_length_60268_cov_150.714143 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5555555555555556 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585821 sample name Hadza_MoBio_hadza-A-D_F_17_1567__NODE_791_length_60268_cov_150.714143 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7737971_virus.634 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11143077 SAMEA13541112 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747084. BACPHLIP temperate score 0.14850677475569002 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541112 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 35.2872 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1546_length_44079_cov_20.186537_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1546_length_44079_cov_20.186537_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745989_virus.1090 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143079 SAMEA13541114 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541114 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 1161.82 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1068_length_56186_cov_644.774439 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; HMM-based (lower-bound) completeness score 56.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1068_length_56186_cov_644.774439 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746101_virus.616 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143080 SAMEA13541115 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541115 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 13.3928 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1355_length_48380_cov_7.803283 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 98.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1355_length_48380_cov_7.803283 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738936_virus.386 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143081 SAMEA13541116 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541116 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 10.8364 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1542_length_44143_cov_5.833091 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1542_length_44143_cov_5.833091 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__MARSEILLE-P3954;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.1542 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143082 SAMEA13541117 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.07747797356828194 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541117 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 33.4222 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1646_length_42180_cov_18.865378 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5217391304347826 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1646_length_42180_cov_18.865378 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738588_bin.338 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71;s__UBA71 sp006954465 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.1646 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143083 SAMEA13541118 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541118 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 52.5599 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1811_length_39650_cov_29.416067 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6451612903225806 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_1811_length_39650_cov_29.416067 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME257298 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.1811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143084 SAMEA13541119 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541119 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 305.289 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1691 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_2072_length_35848_cov_172.035168 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_2072_length_35848_cov_172.035168 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.2072 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143085 SAMEA13541120 336724 Myoviridae environmental samples This sample represents an uncultured Eganvirus virus assembled from ERR7747084. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541120 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 10.8825 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_2455_length_31495_cov_6.054968 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9047619047619048 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_2455_length_31495_cov_6.054968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.2455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Peduovirinae; Eganvirus virus enrichment approach none ERS11143087 SAMEA13541122 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7747084. BACPHLIP temperate score 0.03828965839962564 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541122 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 85.996 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_351_length_104455_cov_47.327627 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9727272727272728 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_351_length_104455_cov_47.327627 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738603_virus.384 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11143088 SAMEA13541123 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541123 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 10.1979 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 25 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_4280_length_20149_cov_5.607613 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_4280_length_20149_cov_5.607613 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.4280 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143089 SAMEA13541124 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541124 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 49.0544 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 264 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_546_length_82639_cov_31.663925 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5306122448979592 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_546_length_82639_cov_31.663925 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159485 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.546 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143090 SAMEA13541125 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541125 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 55.4086 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 187 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_80_length_209283_cov_31.299819 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 8 number of unique standard tRNAs extracted 7 percent of BLAST hits supporting viral taxonomy 0.4065934065934066 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_80_length_209283_cov_31.299819 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.80 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143091 SAMEA13541126 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747125. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541126 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 34.6022 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_246_length_97023_cov_19.850494_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 62.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_246_length_97023_cov_19.850494_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745687_bin.245 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA6382;s__UBA6382 sp900557555 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_provirus.246 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143093 SAMEA13541128 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747125. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541128 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 9.87516 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_1118_length_41786_cov_5.249514 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.66 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8461538461538461 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_1118_length_41786_cov_5.249514 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738599_bin.122 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_virus.1118 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143094 SAMEA13541129 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747125. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541129 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 20.7172 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_1386_length_36395_cov_11.665483 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_1386_length_36395_cov_11.665483 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_virus.875 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143095 SAMEA13541130 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747125. BACPHLIP temperate score 0.1045154185022027 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541130 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 48.4878 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_1939_length_28479_cov_27.527357 Viral contig found in MAG ERR7747125_bin.165 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 52.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_1939_length_28479_cov_27.527357 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738259_provirus.819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143096 SAMEA13541131 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747125. BACPHLIP temperate score 0.09741189427312776 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541131 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 10.0831 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_2873_length_20916_cov_5.977014 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.9 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8666666666666667 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_2873_length_20916_cov_5.977014 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_virus.2873 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143097 SAMEA13541132 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747125. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541132 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 62.982 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 248 Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_576_length_63011_cov_33.728700 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.43243243243243246 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_576_length_63011_cov_33.728700 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745845_bin.299 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541995 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738197_provirus.61 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143098 SAMEA13541133 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747125. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541133 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 15.1567 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_788_length_51946_cov_8.238967 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 88.94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.47368421052631576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_788_length_51946_cov_8.238967 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738557_virus.1534 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143099 SAMEA13541134 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747128. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541134 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 9.4975 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1000_length_50962_cov_5.704510_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 88.32 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.925 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1000_length_50962_cov_5.704510_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738531_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_B;c__Peptococcia;o__Peptococcales;f__Peptococcaceae;g__UMGS1590;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_provirus.931 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143100 SAMEA13541135 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747128. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541135 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 9.65158 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1619_length_36155_cov_5.858168_1 Viral contig found in MAG ERR7747128_bin.67 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 59.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5882352941176471 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1619_length_36155_cov_5.858168_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_provirus.49 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143102 SAMEA13541137 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747128. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541137 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 16.1126 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 461 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_972_length_52224_cov_9.773851_1 Viral contig found in MAG ERR7747128_bin.79 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.55 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_972_length_52224_cov_9.773851_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME253778 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F;s__Eubacterium_F sp003491505 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738269_provirus.475 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143103 SAMEA13541138 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747128. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541138 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 13.5344 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_11921_length_6576_cov_8.359132 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy NA predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_11921_length_6576_cov_8.359132 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747128_virus.11921 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143104 SAMEA13541139 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747128. BACPHLIP temperate score 0.03986784140969163 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541139 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 11.5549 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1396_length_40116_cov_7.025600 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1396_length_40116_cov_7.025600 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738587_virus.1800 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143105 SAMEA13541140 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747128. BACPHLIP temperate score 0.01497797356828193 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541140 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 110.015 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1949_length_31406_cov_72.868046 Viral contig found in MAG ERR7747128_bin.2 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_1949_length_31406_cov_72.868046 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.455 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143106 SAMEA13541141 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747128. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541141 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 13.1041 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_2948_length_22111_cov_7.504902 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_2948_length_22111_cov_7.504902 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7803603_bin.84 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747128_virus.2948 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142776 SAMEA13540810 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746219. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540810 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:33Z INSDC last update 2022-12-27T01:22:33Z INSDC status public MAG coverage depth 29.8006 MAG coverage software Reads (ERR7746219) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559398) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 151 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_M_10_2632__NODE_1128_length_62840_cov_33.320029 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-19 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8775510204081632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586341 sample name Hadza_MoBio_hadza-I-L_M_10_2632__NODE_1128_length_62840_cov_33.320029 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746061_bin.374 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746219_virus.1128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142947 SAMEA13540982 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746688. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540982 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 172.982 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 40 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2037_length_53830_cov_101.106822 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_2037_length_53830_cov_101.106822 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME181333 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900540885 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745759_provirus.941 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142956 SAMEA13540991 2133760 Siphoviridae environmental samples This sample represents an uncultured Streptococcus phage Javan372 virus assembled from ERR7746688. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540991 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 20.0717 MAG coverage software Reads (ERR7746688) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560553) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-E-H_K_24_1920__NODE_4263_length_32974_cov_12.003952 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5208333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586063 sample name Hadza_MoBio_hadza-E-H_K_24_1920__NODE_4263_length_32974_cov_12.003952 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME001139 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus parasanguinis_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746688_virus.4263 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Streptococcus phage Javan372 virus enrichment approach none ERS11142962 SAMEA13540997 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746692. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13540997 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 26.6713 MAG coverage software Reads (ERR7746692) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561431) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_C-REDO_B_7_1518__NODE_200_length_83059_cov_15.357138_1 Viral contig found in MAG ERR7746692_bin.49 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585774 sample name Hadza_MoBio_C-REDO_B_7_1518__NODE_200_length_83059_cov_15.357138_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738555_provirus.57 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142970 SAMEA13541005 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746721. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541005 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:30Z INSDC last update 2022-12-27T01:22:30Z INSDC status public MAG coverage depth 18.4502 MAG coverage software Reads (ERR7746721) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561877) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_F_7_1572__NODE_522_length_38591_cov_9.269876 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS9106181 sample name Hadza_MoBio_hadza-A-D_F_7_1572__NODE_522_length_38591_cov_9.269876 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738628_virus.2595 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142976 SAMEA13541011 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7746739. BACPHLIP temperate score 0.12724256706111475 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541011 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 15.2079 MAG coverage software Reads (ERR7746739) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561457) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_P_1_1512__NODE_311_length_68634_cov_8.958443_1 Viral contig found in MAG ERR7746739_bin.55 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 81.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585768 sample name Hadza_MoBio_hadza-A-D_P_1_1512__NODE_311_length_68634_cov_8.958443_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745906_virus.1378 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142985 SAMEA13541020 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7746741. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541020 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 18.2014 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 32 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1429_length_37733_cov_10.451296 Viral contig found in MAG ERR7746741_bin.65 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_1429_length_37733_cov_10.451296 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.1429 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11142991 SAMEA13541026 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746741. BACPHLIP temperate score 0.35 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541026 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 21.1626 MAG coverage software Reads (ERR7746741) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561599) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_M_8_1180__NODE_606_length_61752_cov_11.835638 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-23 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.95 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8611111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585603 sample name Hadza_MoBio_hadza-A-D_M_8_1180__NODE_606_length_61752_cov_11.835638 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.606 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11142999 SAMEA13541034 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746742. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541034 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 12.5553 MAG coverage software Reads (ERR7746742) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561719) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_J_13_1252__NODE_611_length_50596_cov_6.861854 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-10-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 80.83 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8918918918918919 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585670 sample name Hadza_MoBio_hadza-I-L_J_13_1252__NODE_611_length_50596_cov_6.861854 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746742_virus.611 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143005 SAMEA13541040 926697 uncultured Microviridae This sample represents an uncultured Microviridae sp. virus assembled from ERR7746748. BACPHLIP temperate score 0.02900919059739989 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541040 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 6.89992 MAG coverage software Reads (ERR7746748) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561606) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_MoBio_hadza-A-D_K_12_1156__NODE_16057_length_5466_cov_3.932269 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585580 sample name Hadza_MoBio_hadza-A-D_K_12_1156__NODE_16057_length_5466_cov_3.932269 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.16057 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp. virus enrichment approach none ERS11143014 SAMEA13541049 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541049 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 10.0102 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 36 Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1672_length_37644_cov_5.833524 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5909090909090909 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_1672_length_37644_cov_5.833524 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745947_bin.215 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia;s__Evtepia sp004556345 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.1672 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143020 SAMEA13541055 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746751. BACPHLIP temperate score 0.25627392670077853 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541055 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 159.105 MAG coverage software Reads (ERR7746751) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561748) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_E_23_1060__NODE_675_length_72362_cov_94.604372 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-06 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585484 sample name Hadza_MoBio_hadza-A-D_E_23_1060__NODE_675_length_72362_cov_94.604372 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746751_virus.675 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143028 SAMEA13541063 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746757. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541063 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 7.56616 MAG coverage software Reads (ERR7746757) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561545) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_E_14_1160__NODE_3538_length_16988_cov_4.557980 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.71 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585584 sample name Hadza_MoBio_hadza-A-D_E_14_1160__NODE_3538_length_16988_cov_4.557980 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_provirus.3128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143034 SAMEA13541069 2133760 Siphoviridae environmental samples This sample represents an uncultured Butyrivibrio virus Arawn virus assembled from ERR7746767. BACPHLIP temperate score 0.05119765791341377 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541069 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 7.76377 MAG coverage software Reads (ERR7746767) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560255) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 281 Number of CRISPR spacer hits supporting host taxonomy 510 Submitter Id Hadza_MoBio_hadza-E-H_H_10_2273__NODE_2019_length_31120_cov_3.806333 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 96.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5185185185185185 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_MoBio_hadza-E-H_H_10_2273__NODE_2019_length_31120_cov_3.806333 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745924_provirus.769 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Arawnvirus; Butyrivibrio virus Arawn virus enrichment approach none ERS11143043 SAMEA13541078 1701671 uncultured podovirus This sample represents an uncultured UAG-readthrough crAss clade virus assembled from ERR7746773. BACPHLIP temperate score 0.025 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541078 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 226.017 MAG coverage software Reads (ERR7746773) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560047) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 23 Submitter Id Hadza_MoBio_hadza-E-H_N_21_2138__NODE_229_length_108652_cov_126.728731 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-07-25 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586124 sample name Hadza_MoBio_hadza-E-H_N_21_2138__NODE_229_length_108652_cov_126.728731 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746773_virus.229 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade virus enrichment approach none ERS11143049 SAMEA13541084 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7746779. BACPHLIP temperate score 0.11693695284855372 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541084 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:29Z INSDC last update 2022-12-27T01:22:29Z INSDC status public MAG coverage depth 39.3843 MAG coverage software Reads (ERR7746779) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 63 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-I-L_K_1_2479__NODE_907_length_55316_cov_22.351219_1 Viral contig found in MAG ERR7746779_bin.106 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586253 sample name Hadza_MoBio_hadza-I-L_K_1_2479__NODE_907_length_55316_cov_22.351219_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_virus.1910 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143057 SAMEA13541092 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7746785. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541092 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 9.87953 MAG coverage software Reads (ERR7746785) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561612) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 143 Number of CRISPR spacer hits supporting host taxonomy 1651 Submitter Id Hadza_MoBio_hadza-A-D_N_3_1523__NODE_1723_length_35537_cov_5.604766 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-26 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.58 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585778 sample name Hadza_MoBio_hadza-A-D_N_3_1523__NODE_1723_length_35537_cov_5.604766 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0362748 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143063 SAMEA13541098 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7746793. BACPHLIP temperate score 0.25702505857542585 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541098 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 11.0672 MAG coverage software Reads (ERR7746793) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 42 Submitter Id Hadza_MoBio_hadza-A-D_D_17_1579__NODE_1166_length_35452_cov_6.957965 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 91.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585828 sample name Hadza_MoBio_hadza-A-D_D_17_1579__NODE_1166_length_35452_cov_6.957965 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME269197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615;s__KLE1615 sp900066985 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.2363 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143072 SAMEA13541107 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747083. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541107 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T01:22:28Z INSDC last update 2022-12-27T01:22:28Z INSDC status public MAG coverage depth 17.9905 MAG coverage software Reads (ERR7747083) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4566884) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 169 Number of CRISPR spacer hits supporting host taxonomy 48 Submitter Id Hadza_MoBio_hadza-A-D_F_17_1567__NODE_1199_length_46075_cov_10.831232 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-28 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585821 sample name Hadza_MoBio_hadza-A-D_F_17_1567__NODE_1199_length_46075_cov_10.831232 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.1185 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143078 SAMEA13541113 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747084. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541113 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 9.56116 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 45 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_364_length_102141_cov_5.296726_1 Viral contig found in MAG ERR7747084_bin.185 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.04 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_364_length_102141_cov_5.296726_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738251_virus.875 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143086 SAMEA13541121 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747084. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541121 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 52.7386 MAG coverage software Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 95 Submitter Id Hadza_MoBio_hadza-A-D_K_14_1158__NODE_2946_length_27344_cov_29.938204 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2013-09-08 completeness approach CheckV; AAI-based (high-confidence) completeness score 50.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8181818181818182 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585582 sample name Hadza_MoBio_hadza-A-D_K_14_1158__NODE_2946_length_27344_cov_29.938204 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME204972 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900539625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.1159 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143092 SAMEA13541127 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747125. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541127 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 73.0913 MAG coverage software Reads (ERR7747125) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560347) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-E-H_K_21_1780__NODE_60_length_168389_cov_40.205571_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-05-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586002 sample name Hadza_MoBio_hadza-E-H_K_21_1780__NODE_60_length_168389_cov_40.205571_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747125_provirus.60 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143101 SAMEA13541136 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747128. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541136 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 504.952 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 19 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_51_length_205871_cov_314.071236_1 Viral contig found in MAG ERR7747128_bin.20 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 94 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_51_length_205871_cov_314.071236_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745625_provirus.431 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143107 SAMEA13541142 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7747128. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541142 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 14.4561 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_4303_length_15742_cov_8.638940 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 70.54 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_4303_length_15742_cov_8.638940 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.8114 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11143108 SAMEA13541143 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747128. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541143 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 196.662 MAG coverage software Reads (ERR7747128) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559679) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_L_2_2317__NODE_751_length_61576_cov_119.023968 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586189 sample name Hadza_MoBio_hadza-E-H_L_2_2317__NODE_751_length_61576_cov_119.023968 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746436_virus.373 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143109 SAMEA13541144 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7747140. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541144 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 24.2031 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 55 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1094_length_57285_cov_14.870770_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; HMM-based (lower-bound) completeness score 60.82 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1094_length_57285_cov_14.870770_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.1350 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143110 SAMEA13541145 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747140. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541145 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 34.231 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 33 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_168_length_141384_cov_20.419080_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_168_length_141384_cov_20.419080_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_provirus.168 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143111 SAMEA13541146 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7747140. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541146 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 198.761 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 13 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_408_length_95527_cov_122.685186_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 44.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6923076923076923 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_408_length_95527_cov_122.685186_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738223_provirus.260 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143112 SAMEA13541147 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747140. BACPHLIP temperate score 0.7524779735682819 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541147 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 43.6811 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 63 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_819_length_67122_cov_26.562070_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7941176470588235 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_819_length_67122_cov_26.562070_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME140265 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia;s__Blautia stercoris vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_provirus.819 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143113 SAMEA13541148 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747140. BACPHLIP temperate score 0.45473568281938326 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541148 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 46.8722 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1093_length_57292_cov_27.921314 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1093_length_57292_cov_27.921314 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738191_bin.68 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900545245 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.1525 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143114 SAMEA13541149 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747140. BACPHLIP temperate score 0.10029736837256067 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541149 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 710.43 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1278_length_52324_cov_423.865715 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1278_length_52324_cov_423.865715 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746411_bin.453 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.1278 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143115 SAMEA13541150 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7747140. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541150 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 11.5305 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1723_length_43559_cov_7.065958 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5483870967741935 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_1723_length_43559_cov_7.065958 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME251083 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger qucibialis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.1723 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11143116 SAMEA13541151 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7747140. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541151 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 13.2061 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 73 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_195_length_133840_cov_7.993982 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.6458333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_195_length_133840_cov_7.993982 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.195 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11143117 SAMEA13541152 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747140. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541152 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 29.0798 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 24 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_2223_length_36647_cov_17.472136 Viral contig found in MAG ERR7747140_bin.350 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_2223_length_36647_cov_17.472136 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME124777 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;s__Dysosmobacter sp001916835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746217_virus.1986 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143118 SAMEA13541153 2133760 Siphoviridae environmental samples This sample represents an uncultured Vegasvirus virus assembled from ERR7747140. BACPHLIP temperate score 0.15395275377695644 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541153 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 25.4577 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 20 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_2372_length_35211_cov_15.860135 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6129032258064516 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_2372_length_35211_cov_15.860135 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.2372 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Gochnauervirinae; Vegasvirus virus enrichment approach none ERS11143119 SAMEA13541154 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747140. BACPHLIP temperate score 0.0505538234328848 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541154 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 20.2088 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_2776_length_31776_cov_11.788448 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_2776_length_31776_cov_11.788448 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0353882 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143120 SAMEA13541155 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747140. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541155 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 163.627 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 364 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_324_length_105603_cov_100.295093 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.2857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_324_length_105603_cov_100.295093 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143121 SAMEA13541156 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7747140. BACPHLIP temperate score 0.09223568281938328 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541156 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 225.359 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_4156_length_24020_cov_241.475045 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (medium-confidence) completeness score 61.25 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_4156_length_24020_cov_241.475045 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;unk;unk;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.4156 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11143122 SAMEA13541157 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7747140. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541157 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 11.6456 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_517_length_86103_cov_6.784530 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.575 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_517_length_86103_cov_6.784530 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.517 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11143123 SAMEA13541158 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7747140. BACPHLIP temperate score 0.5875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541158 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 79.8088 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_73_length_195331_cov_47.029561 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 32 number of unique standard tRNAs extracted 18 percent of BLAST hits supporting viral taxonomy 0.7538461538461538 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_73_length_195331_cov_47.029561 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.73 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11143124 SAMEA13541159 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747140. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541159 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 22.0777 MAG coverage software Reads (ERR7747140) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560474) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 27 Number of CRISPR spacer hits supporting host taxonomy 2276 Submitter Id Hadza_MoBio_hadza-E-H_C_4_1831__NODE_984_length_60560_cov_13.123870 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-05 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5357142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586027 sample name Hadza_MoBio_hadza-E-H_C_4_1831__NODE_984_length_60560_cov_13.123870 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747140_virus.984 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143125 SAMEA13541160 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747255. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541160 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 19.5381 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 60 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_18_length_366877_cov_11.615319_1 Viral contig found in MAG ERR7747255_bin.223 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 96.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8846153846153846 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_18_length_366877_cov_11.615319_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738608_bin.72 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_provirus.18 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143126 SAMEA13541161 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses provirus assembled from ERR7747255. BACPHLIP temperate score 0.325 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541161 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 22.0748 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_243_length_130216_cov_13.743920_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.92 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_243_length_130216_cov_13.743920_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738258_provirus.141 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11143127 SAMEA13541162 1701671 uncultured podovirus This sample represents an uncultured Podoviridae provirus assembled from ERR7747255. BACPHLIP temperate score 0.8125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541162 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 40.019 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 173 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_600_length_82223_cov_24.572542_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_600_length_82223_cov_24.572542_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_provirus.600 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11143128 SAMEA13541163 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7747255. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541163 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 18.4118 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_12324_length_11095_cov_10.781060 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 94.53 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_12324_length_11095_cov_10.781060 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745582_bin.96 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.12324 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11143129 SAMEA13541164 2100421 uncultured Caudovirales phage This sample represents an uncultured Autographiviridae virus assembled from ERR7747255. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541164 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 22.8698 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 18 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_1740_length_44625_cov_13.367895 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_1740_length_44625_cov_13.367895 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746398_virus.1478 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Autographiviridae virus enrichment approach none ERS11143130 SAMEA13541165 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis virus assembled from ERR7747255. BACPHLIP temperate score 0.3 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541165 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 32.2096 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 35 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_1956_length_41224_cov_20.282038 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 70.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_1956_length_41224_cov_20.282038 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.1133 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11143131 SAMEA13541166 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747255. BACPHLIP temperate score 0.1125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541166 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 17.5914 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 6 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_224_length_133540_cov_10.623416 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 63.72 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_224_length_133540_cov_10.623416 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738580_bin.236 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668;s__UMGS1668 sp900553955 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746741_virus.125 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143132 SAMEA13541167 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747255. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541167 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 12.7006 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_2452_length_35771_cov_8.595086 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_2452_length_35771_cov_8.595086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738629_provirus.570 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143133 SAMEA13541168 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747255. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541168 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 10.5097 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_2923_length_32170_cov_6.052940 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 58.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_2923_length_32170_cov_6.052940 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME098969 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia sp900542795 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.2923 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143134 SAMEA13541169 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747255. BACPHLIP temperate score 0.275 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541169 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 9.93317 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_3542_length_28385_cov_5.728416 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 51.86 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_3542_length_28385_cov_5.728416 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738230_bin.158 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter_A;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745419_virus.1042 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143135 SAMEA13541170 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747255. BACPHLIP temperate score 0.0375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541170 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 7.19971 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_4176_length_25136_cov_3.939383 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_4176_length_25136_cov_3.939383 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.4176 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143136 SAMEA13541171 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747255. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541171 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 9.52685 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_4821_length_22756_cov_5.668504 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 98.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_4821_length_22756_cov_5.668504 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747255_virus.4821 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143137 SAMEA13541172 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747255. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541172 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 12.7474 MAG coverage software Reads (ERR7747255) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567690) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_833_length_68788_cov_7.491086 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.09 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 14 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.5116279069767442 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586192 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_14_2320__NODE_833_length_68788_cov_7.491086 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0380017 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143138 SAMEA13541173 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747322. BACPHLIP temperate score 0.10303179700116676 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541173 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 74.3278 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 516 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_1231_length_44379_cov_46.330685_1 Viral contig found in MAG ERR7747322_bin.160 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.06 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_1231_length_44379_cov_46.330685_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738566_bin.143 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__Treponema_D sp900541945 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_provirus.1231 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143139 SAMEA13541174 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747322. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541174 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 184.893 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 47 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_266_length_97570_cov_117.825885_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5238095238095238 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_266_length_97570_cov_117.825885_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_provirus.266 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143140 SAMEA13541175 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747322. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541175 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 19.7225 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 141 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_436_length_76659_cov_12.224034_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7857142857142857 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_436_length_76659_cov_12.224034_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME112856 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp003447235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738554_virus.68 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143141 SAMEA13541176 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Epona provirus assembled from ERR7747322. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541176 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 11.2638 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 82 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_866_length_53857_cov_6.632875_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (medium-confidence) completeness score 97.27 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_866_length_53857_cov_6.632875_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143157 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q;s__Clostridium_Q sp003024715 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_provirus.866 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Eponavirus; Faecalibacterium virus Epona virus enrichment approach none ERS11143142 SAMEA13541177 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747322. BACPHLIP temperate score 0.7625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541177 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 8.65944 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 21 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_1321_length_42668_cov_4.975699 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.47619047619047616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_1321_length_42668_cov_4.975699 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_virus.1510 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143143 SAMEA13541178 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus virus assembled from ERR7747322. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541178 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 450.299 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3475 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_1944_length_33064_cov_263.731015 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 61.8 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.782608695652174 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_1944_length_33064_cov_263.731015 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME145417 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_virus.1944 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11143144 SAMEA13541179 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747322. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541179 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 11.8828 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_2754_length_26270_cov_7.079143 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.43 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_2754_length_26270_cov_7.079143 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747322_virus.2754 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143145 SAMEA13541180 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747322. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541180 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 11.7869 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_594_length_65268_cov_6.845500 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_594_length_65268_cov_6.845500 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738588_virus.1048 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143146 SAMEA13541181 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747322. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541181 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 32.797 MAG coverage software Reads (ERR7747322) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560430) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 11 Submitter Id Hadza_MoBio_hadza-E-H_A_20_1823__NODE_830_length_55031_cov_20.336390 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-02 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586023 sample name Hadza_MoBio_hadza-E-H_A_20_1823__NODE_830_length_55031_cov_20.336390 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME128517 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900290275 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738493_virus.834 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143147 SAMEA13541182 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747324. BACPHLIP temperate score 0.2625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541182 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 99.0223 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 55 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_112_length_174131_cov_65.079113_1 Viral contig found in MAG ERR7747324_bin.83 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 95.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8780487804878049 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_112_length_174131_cov_65.079113_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738571_virus.1369 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143148 SAMEA13541183 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747324. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541183 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 15.8617 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 174 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2891_length_30274_cov_8.979303_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.87 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8421052631578947 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2891_length_30274_cov_8.979303_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME085241 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;s__Holdemanella biformis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_provirus.2891 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143149 SAMEA13541184 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7747324. BACPHLIP temperate score 0.11996874984972046 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541184 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 17.4659 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_10675_length_11896_cov_10.098232 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; ITR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_10675_length_11896_cov_10.098232 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738570_virus.11112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11143150 SAMEA13541185 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747324. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541185 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 20.7712 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_1243_length_52097_cov_12.063149 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.6341463414634146 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_1243_length_52097_cov_12.063149 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_virus.808 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143151 SAMEA13541186 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747324. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541186 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 27.5194 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_1464_length_46733_cov_16.586034 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_1464_length_46733_cov_16.586034 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738581_virus.1943 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143152 SAMEA13541187 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747324. BACPHLIP temperate score 0.9 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541187 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 108.027 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 132 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_1828_length_40353_cov_69.070191 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.08 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_1828_length_40353_cov_69.070191 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0359261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143153 SAMEA13541188 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747324. BACPHLIP temperate score 0.01299472295514512 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541188 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 14.8273 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 30 Number of CRISPR spacer hits supporting host taxonomy 61 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2036_length_37475_cov_8.703380 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 87.63 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2036_length_37475_cov_8.703380 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.2036 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143154 SAMEA13541189 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747324. BACPHLIP temperate score 0.0625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541189 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 60.5918 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 39 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2425_length_33712_cov_35.529776 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 74.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2425_length_33712_cov_35.529776 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0256792 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143155 SAMEA13541190 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747324. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541190 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 12.0506 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 53 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2757_length_31118_cov_7.075062 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_2757_length_31118_cov_7.075062 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME159035 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp900317525 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0240719 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143156 SAMEA13541191 340016 uncultured virus This sample represents an uncultured Roseburia phage Jekyll virus assembled from ERR7747324. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541191 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 7.99452 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 12 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_3365_length_27154_cov_4.571297 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.24 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type uncharacterized project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_3365_length_27154_cov_4.571297 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738602_bin.29 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor;s__Acetatifactor sp900554205 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738252_provirus.1014 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; unclassified bacterial viruses; Roseburia phage Jekyll virus enrichment approach none ERS11143157 SAMEA13541192 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747324. BACPHLIP temperate score 0.14970084156959676 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541192 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 13.0373 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 17 Number of CRISPR spacer hits supporting host taxonomy 68 Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_4063_length_23780_cov_7.451842 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.88 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_4063_length_23780_cov_7.451842 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.4063 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143158 SAMEA13541193 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747324. BACPHLIP temperate score 0.5375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541193 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 29.8843 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_584_length_80651_cov_18.217787 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; HMM-based (lower-bound) completeness score 87.39 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_584_length_80651_cov_18.217787 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745594_virus.465 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143159 SAMEA13541194 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7747324. BACPHLIP temperate score 0.02187416669562399 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541194 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 48.1867 MAG coverage software Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_A_18_1822__NODE_9746_length_12698_cov_27.857460 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-06-01 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586022 sample name Hadza_MoBio_hadza-E-H_A_18_1822__NODE_9746_length_12698_cov_27.857460 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747324_virus.9746 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11143160 SAMEA13541195 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747394. BACPHLIP temperate score 0.22703565487607813 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541195 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 13.0253 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 258 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1397_length_52550_cov_7.642464_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 5 number of unique standard tRNAs extracted 5 percent of BLAST hits supporting viral taxonomy 0.4090909090909091 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1397_length_52550_cov_7.642464_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME111561 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_provirus.1397 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143161 SAMEA13541196 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747394. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541196 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 122.669 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 120 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1768_length_45995_cov_75.705932_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.896551724137931 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1768_length_45995_cov_75.705932_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738559_provirus.1426 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143162 SAMEA13541197 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae provirus assembled from ERR7747394. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541197 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:33Z INSDC last update 2022-12-27T04:22:33Z INSDC status public MAG coverage depth 34.3934 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 9 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_233_length_124647_cov_19.942554_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 89.22 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_233_length_124647_cov_19.942554_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738586_virus.660 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143163 SAMEA13541198 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747394. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541198 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 52.1149 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 49 Number of CRISPR spacer hits supporting host taxonomy 20 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_337_length_107053_cov_30.608062_1 Viral contig found in MAG ERR7747394_bin.425 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 82.29 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_337_length_107053_cov_30.608062_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_provirus.337 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143164 SAMEA13541199 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747394. BACPHLIP temperate score 0.13934525602217446 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541199 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 9.37412 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_471_length_91379_cov_5.170467_1 Viral contig found in MAG ERR7747394_bin.23 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 57.52 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9565217391304348 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_471_length_91379_cov_5.170467_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738657_bin.225 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Monoglobales_A;f__UBA1381;g__RQCD01;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738146_provirus.143 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143165 SAMEA13541200 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747394. BACPHLIP temperate score 0.675 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541200 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 10.7641 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_797_length_71434_cov_6.139258_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_797_length_71434_cov_6.139258_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1228 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143166 SAMEA13541201 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541201 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 15.2077 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 481 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1137_length_58899_cov_8.704192 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 97.18 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.6451612903225806 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1137_length_58899_cov_8.704192 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745335_virus.1195 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143167 SAMEA13541202 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541202 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 70.1165 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1447_length_51799_cov_40.846526 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.99 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.631578947368421 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_1447_length_51799_cov_40.846526 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738167_virus.348 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143168 SAMEA13541203 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.10203249223614484 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541203 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 18.5828 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_2053_length_42217_cov_11.298434 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.91 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7368421052631579 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_2053_length_42217_cov_11.298434 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746757_bin.199 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__UBA1436;s__UBA1436 sp900541355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.1243 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143169 SAMEA13541204 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.00379359296842034 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541204 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 9.53292 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 106 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_2615_length_36829_cov_5.316228 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9285714285714286 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_2615_length_36829_cov_5.316228 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000676 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;s__Blautia_A massiliensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.2615 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143170 SAMEA13541205 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.0346637675235751 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541205 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 20.887 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_2960_length_34477_cov_12.253401 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 93.67 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_2960_length_34477_cov_12.253401 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738596_provirus.332 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143171 SAMEA13541206 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541206 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 10.8138 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 2 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_3759_length_29764_cov_6.032001 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.98 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.3 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_3759_length_29764_cov_6.032001 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.3759 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143172 SAMEA13541207 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.1875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541207 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 38.8878 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 969 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_4462_length_26661_cov_22.396329 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 75.16 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_4462_length_26661_cov_22.396329 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME018576 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000433355 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746767_virus.2138 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143173 SAMEA13541208 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541208 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 8.117 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_5031_length_24714_cov_4.504242 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 73.33 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9166666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_5031_length_24714_cov_4.504242 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.5031 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143174 SAMEA13541209 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747394. BACPHLIP temperate score 0.0024238520115018 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541209 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 19.9526 MAG coverage software Reads (ERR7747394) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567788) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 348 Submitter Id Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_7503_length_18848_cov_11.782004 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 77.03 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7894736842105263 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586170 sample name Hadza_PheChl_Fiber-Hadza-Nepal_C_8_2273__NODE_7503_length_18848_cov_11.782004 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME196077 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747394_virus.7503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143175 SAMEA13541210 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747426. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541210 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 29.2569 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 94 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_1165_length_72402_cov_34.379551_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8947368421052632 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_1165_length_72402_cov_34.379551_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_provirus.1165 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143176 SAMEA13541211 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747426. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541211 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 35.6472 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 49 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_183_length_189874_cov_20.766082_1 Viral contig found in MAG ERR7747426_bin.236 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_183_length_189874_cov_20.766082_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738143_provirus.882 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143177 SAMEA13541212 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747426. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541212 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 40.526 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 22 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_28_length_369314_cov_24.384404_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 16 number of unique standard tRNAs extracted 12 percent of BLAST hits supporting viral taxonomy 0.5818181818181818 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_28_length_369314_cov_24.384404_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738176_bin.74 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738461_virus.76 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143178 SAMEA13541213 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747426. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541213 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 87.0369 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 293 Number of CRISPR spacer hits supporting host taxonomy 132 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_453_length_127034_cov_54.007987_1 Viral contig found in MAG ERR7747426_bin.212 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; HMM-based (lower-bound) completeness score 89.79 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_453_length_127034_cov_54.007987_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738179_provirus.207 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143179 SAMEA13541214 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747426. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541214 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 21.4627 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 22 Number of CRISPR spacer hits supporting host taxonomy 72 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_939_length_83724_cov_12.728765_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 69.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_939_length_83724_cov_12.728765_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745903_provirus.800 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143180 SAMEA13541215 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Oengus virus assembled from ERR7747426. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541215 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 818.883 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_1488_length_62021_cov_484.274571 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9482758620689656 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_1488_length_62021_cov_484.274571 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738608_virus.1393 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Oengusvirus; Faecalibacterium virus Oengus virus enrichment approach none ERS11143181 SAMEA13541216 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747426. BACPHLIP temperate score 0.07736784140969163 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541216 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 10.1191 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 217 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_1764_length_54715_cov_5.919287 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 65.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_1764_length_54715_cov_5.919287 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738239_virus.269 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143182 SAMEA13541217 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747426. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541217 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 201.548 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_210_length_181367_cov_130.218633 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 56.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 13 number of unique standard tRNAs extracted 12 percent of BLAST hits supporting viral taxonomy 0.640625 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_210_length_181367_cov_130.218633 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.210 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143183 SAMEA13541218 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747426. BACPHLIP temperate score 0.925 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541218 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 14.288 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 112 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_2503_length_41686_cov_8.790045 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.05 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_2503_length_41686_cov_8.790045 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.2503 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143184 SAMEA13541219 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747426. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541219 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 13.2622 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_2731_length_39316_cov_7.972706 Viral contig found in MAG ERR7747426_bin.428 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 90.37 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_2731_length_39316_cov_7.972706 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747426_virus.2731 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143185 SAMEA13541220 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747426. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541220 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 38.0535 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 25 Number of CRISPR spacer hits supporting host taxonomy 96 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_2891_length_37697_cov_23.335486 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 92.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8275862068965517 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_2891_length_37697_cov_23.335486 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745835_bin.156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A;s__Butyricicoccus_A sp002395695 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.2122 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143186 SAMEA13541221 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747426. BACPHLIP temperate score 0.5125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541221 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 9.81548 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 10 Number of CRISPR spacer hits supporting host taxonomy 15 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_3678_length_30753_cov_5.544074 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 91.12 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7647058823529411 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_3678_length_30753_cov_5.544074 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter;s__;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738218_virus.1048 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143187 SAMEA13541222 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747426. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541222 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 41.8144 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 52 Number of CRISPR spacer hits supporting host taxonomy 67 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_4926_length_24014_cov_24.985629 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 71.28 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_4926_length_24014_cov_24.985629 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738179_virus.1723 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143188 SAMEA13541223 2100421 uncultured Caudovirales phage This sample represents an uncultured Salasmaviridae virus assembled from ERR7747426. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541223 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 24.8424 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_6494_length_18948_cov_14.767156 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 99.36 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_6494_length_18948_cov_14.767156 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747084_virus.4536 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Salasmaviridae virus enrichment approach none ERS11143189 SAMEA13541224 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747426. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541224 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 7.6437 MAG coverage software Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 6 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-I-L_I_19_2477__NODE_9565_length_13577_cov_4.467556 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (medium-confidence) completeness score 64.26 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586251 sample name Hadza_MoBio_hadza-I-L_I_19_2477__NODE_9565_length_13577_cov_4.467556 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738624_virus.9966 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143190 SAMEA13541225 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747522. BACPHLIP temperate score 0.3625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541225 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 21.9016 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 57 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_1547_length_51062_cov_13.563872_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 94.62 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_1547_length_51062_cov_13.563872_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.1032 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143191 SAMEA13541226 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747522. BACPHLIP temperate score 0 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541226 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 8.93346 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2135_length_41072_cov_5.393341_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 72.35 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4444444444444444 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2135_length_41072_cov_5.393341_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738957_bin.179 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_provirus.2135 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143192 SAMEA13541227 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747522. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541227 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 11.2969 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 43 Number of CRISPR spacer hits supporting host taxonomy 103 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_506_length_99069_cov_6.733736_1 Viral contig found in MAG ERR7747522_bin.208 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.34 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9130434782608696 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_506_length_99069_cov_6.733736_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746345_bin.167 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-460;s__CAG-460 sp000437315 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738187_provirus.645 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143193 SAMEA13541228 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747522. BACPHLIP temperate score 0.9125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541228 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 13.7017 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 83 Number of CRISPR spacer hits supporting host taxonomy 26 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_979_length_68493_cov_8.298848_1 Viral contig found in MAG ERR7747522_bin.240 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7096774193548387 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_979_length_68493_cov_8.298848_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738553_virus.1446 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143194 SAMEA13541229 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747522. BACPHLIP temperate score 0.827477973568282 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541229 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 39.8028 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 629 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_1402_length_54192_cov_24.951141 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.52 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_1402_length_54192_cov_24.951141 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738651_virus.1381 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143195 SAMEA13541230 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747522. BACPHLIP temperate score 0.9625 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541230 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 24.8713 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 0 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_1749_length_47237_cov_15.041243 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8936170212765957 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_1749_length_47237_cov_15.041243 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738606_bin.280 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1217;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_virus.1749 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143196 SAMEA13541231 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747522. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541231 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 65.1139 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 52 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2000_length_42890_cov_40.033962 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2000_length_42890_cov_40.033962 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746793_virus.873 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143197 SAMEA13541232 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747522. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541232 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 11.0379 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 11 Number of CRISPR spacer hits supporting host taxonomy 14 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2315_length_38673_cov_6.762722 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2315_length_38673_cov_6.762722 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME143156 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus faecis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738561_virus.1125 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143198 SAMEA13541233 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747522. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541233 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 10.7425 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 4 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2540_length_36063_cov_6.414911 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.76 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_2540_length_36063_cov_6.414911 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_provirus.38 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143199 SAMEA13541234 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747522. BACPHLIP temperate score 0.17658177410957304 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541234 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 13.7346 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_3042_length_31461_cov_8.233463 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 56.69 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_3042_length_31461_cov_8.233463 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738631_virus.1175 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143200 SAMEA13541235 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747522. BACPHLIP temperate score 0.29686123348017607 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541235 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 63.5789 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 227 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_4045_length_25130_cov_38.705903 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (high-confidence) completeness score 60.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_4045_length_25130_cov_38.705903 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738610_provirus.918 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143201 SAMEA13541236 1701671 uncultured podovirus This sample represents an uncultured crAssphage cr8_1 virus assembled from ERR7747522. BACPHLIP temperate score 0.12878892628021937 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541236 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 287.337 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_516_length_98777_cov_172.968531 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_516_length_98777_cov_172.968531 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738515_bin.43 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746012_virus.107 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; crAssphage cr8_1 virus enrichment approach none ERS11143202 SAMEA13541237 1701671 uncultured podovirus This sample represents an uncultured unclassified Astrithrvirus virus assembled from ERR7747522. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541237 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 14.302 MAG coverage software Reads (ERR7747522) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561110) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_D_19_1578__NODE_8526_length_13475_cov_8.609494 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-01-30 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585827 sample name Hadza_MoBio_hadza-A-D_D_19_1578__NODE_8526_length_13475_cov_8.609494 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME116287 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281;s__UBA10281 sp900767815 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747522_virus.8526 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; Astrithrvirus; unclassified Astrithrvirus virus enrichment approach none ERS11143203 SAMEA13541238 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lagaffe provirus assembled from ERR7747615. BACPHLIP temperate score 0.125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541238 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 16.418 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 372 Number of CRISPR spacer hits supporting host taxonomy 59 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_1252_length_51154_cov_10.070462_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 99.1 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.9692307692307692 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_1252_length_51154_cov_10.070462_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0372952 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Lagaffevirus; Faecalibacterium virus Lagaffe virus enrichment approach none ERS11143204 SAMEA13541239 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7747615. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541239 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 1887.37 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_1752_length_39660_cov_1368.283986_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 53.74 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_1752_length_39660_cov_1368.283986_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME108259 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900313215 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738604_provirus.763 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143205 SAMEA13541240 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Taranis provirus assembled from ERR7747615. BACPHLIP temperate score 0.2125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541240 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 222.384 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 61 Number of CRISPR spacer hits supporting host taxonomy 453 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_523_length_90767_cov_140.001875_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.15 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7297297297297297 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_523_length_90767_cov_140.001875_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738264_virus.805 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Taranisvirus; Faecalibacterium virus Taranis virus enrichment approach none ERS11143206 SAMEA13541241 2133760 Siphoviridae environmental samples This sample represents an uncultured Spbetavirus virus assembled from ERR7747615. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541241 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 77.2983 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 65 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_112_length_191100_cov_48.351183 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 35 number of unique standard tRNAs extracted 20 percent of BLAST hits supporting viral taxonomy 0.7534246575342466 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_112_length_191100_cov_48.351183 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747615_virus.112 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus virus enrichment approach none ERS11143207 SAMEA13541242 1478972 Gokushovirinae environmental samples This sample represents an uncultured Chlamydiamicrovirus virus assembled from ERR7747615. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541242 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 39.5313 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_16257_length_5529_cov_26.178283 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type ssDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_16257_length_5529_cov_26.178283 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747615_virus.16257 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; Gokushovirinae; Chlamydiamicrovirus virus enrichment approach none ERS11143208 SAMEA13541243 2133760 Siphoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Lugh virus assembled from ERR7747615. BACPHLIP temperate score 0.825 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541243 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 15.0699 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 17 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_2052_length_35085_cov_8.990374 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 86.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_2052_length_35085_cov_8.990374 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747615_virus.2052 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Lughvirus; Faecalibacterium virus Lugh virus enrichment approach none ERS11143209 SAMEA13541244 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747615. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541244 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 7.02321 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 166 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_2632_length_28627_cov_4.180175 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 63.44 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7333333333333333 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_2632_length_28627_cov_4.180175 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0347707 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143210 SAMEA13541245 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747615. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541245 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 13.4212 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 32 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_471_length_96134_cov_8.434711 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.51 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9772727272727272 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_471_length_96134_cov_8.434711 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747615_virus.471 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143211 SAMEA13541246 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7747615. BACPHLIP temperate score 0.725 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541246 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 9.51713 MAG coverage software Reads (ERR7747615) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559937) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 195 Submitter Id Hadza_MoBio_hadza-I-L_M_19_2499__NODE_743_length_73507_cov_6.020809 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-16 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 0.6792452830188679 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586273 sample name Hadza_MoBio_hadza-I-L_M_19_2499__NODE_743_length_73507_cov_6.020809 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000247 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter;s__Intestinibacter bartlettii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745819_virus.561 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143212 SAMEA13541247 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747782. BACPHLIP temperate score 0.4375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541247 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 294.416 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 12 Number of CRISPR spacer hits supporting host taxonomy 317 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_1166_length_67350_cov_187.902918_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.5517241379310345 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_1166_length_67350_cov_187.902918_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738270_virus.391 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143213 SAMEA13541248 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747782. BACPHLIP temperate score 0.24217479228380095 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541248 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 27.8632 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 28 Number of CRISPR spacer hits supporting host taxonomy 531 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_1855_length_48494_cov_16.851808_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.57 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8888888888888888 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_1855_length_48494_cov_16.851808_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000977 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus;s__Coprococcus eutactus_A vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_provirus.1855 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143214 SAMEA13541249 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747782. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541249 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:34Z INSDC last update 2022-12-27T04:22:34Z INSDC status public MAG coverage depth 228.881 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 30 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_2857_length_34638_cov_128.357918_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 68.85 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_2857_length_34638_cov_128.357918_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME142596 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotellamassilia;s__Prevotellamassilia timonensis vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_provirus.2857 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143215 SAMEA13541250 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747782. BACPHLIP temperate score 0.06486784140969165 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541250 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 10.1117 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 8 Number of CRISPR spacer hits supporting host taxonomy 18 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_503_length_110883_cov_5.634189_1 Viral contig found in MAG ERR7747782_bin.194 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 84.76 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4615384615384616 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_503_length_110883_cov_5.634189_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738275_provirus.24 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143216 SAMEA13541251 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7747782. BACPHLIP temperate score 0.18368843659633977 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541251 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 86.4069 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 28 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_96_length_236029_cov_48.849851_1 Viral contig found in MAG ERR7747782_bin.151 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 89.96 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_96_length_236029_cov_48.849851_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-245;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738274_virus.1718 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143217 SAMEA13541252 1701671 uncultured podovirus This sample represents an uncultured Podoviridae virus assembled from ERR7747782. BACPHLIP temperate score 0.03878438135477076 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541252 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 19.4446 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 3 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_162_length_190958_cov_10.868400 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 9 number of unique standard tRNAs extracted 8 percent of BLAST hits supporting viral taxonomy 0.48148148148148145 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_162_length_190958_cov_10.868400 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7747782_virus.162 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae virus enrichment approach none ERS11143218 SAMEA13541253 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747782. BACPHLIP temperate score 0.2375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541253 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 86.6653 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_209_length_172865_cov_50.527027 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; HMM-based (lower-bound) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 3 number of unique standard tRNAs extracted 3 percent of BLAST hits supporting viral taxonomy 1 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_209_length_172865_cov_50.527027 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738957_virus.128 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143219 SAMEA13541254 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales virus assembled from ERR7747782. BACPHLIP temperate score 0.07619765791341378 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541254 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 761.603 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 29 Number of CRISPR spacer hits supporting host taxonomy 4 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_2446_length_39534_cov_436.002129 Viral contig found in MAG ERR7747782_bin.274 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8571428571428571 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_2446_length_39534_cov_436.002129 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745291_bin.408 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16;s__RF16 sp900556095 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738235_virus.1304 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143220 SAMEA13541255 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7747782. BACPHLIP temperate score 0.1405180011700873 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541255 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 283.735 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 85 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_2807_length_35265_cov_166.036035 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (high-confidence) completeness score 52.41 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_2807_length_35265_cov_166.036035 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745423_virus.493 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11143221 SAMEA13541256 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7747782. BACPHLIP temperate score 0.0752082847671273 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541256 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 89.8275 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_3626_length_28496_cov_51.834582 Viral contig found in MAG ERR7747782_bin.141 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; AAI-based (medium-confidence) completeness score 63.73 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8823529411764706 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_3626_length_28496_cov_51.834582 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738256_bin.97 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp000436915 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745994_virus.2075 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143222 SAMEA13541257 1701671 uncultured podovirus This sample represents an uncultured crAss-like viruses virus assembled from ERR7747782. BACPHLIP temperate score 0.15 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541257 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 14.5678 MAG coverage software Reads (ERR7747782) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559595) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 69 Submitter Id Hadza_MoBio_hadza-E-H_J_6_2308__NODE_576_length_104147_cov_8.097310 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz collection_date 2014-08-12 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 18 number of unique standard tRNAs extracted 15 percent of BLAST hits supporting viral taxonomy 0.9078947368421052 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2586180 sample name Hadza_MoBio_hadza-E-H_J_6_2308__NODE_576_length_104147_cov_8.097310 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738601_virus.368 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses virus enrichment approach none ERS11143223 SAMEA13541258 336724 Myoviridae environmental samples This sample represents an uncultured Faecalibacterium virus Mushu provirus assembled from ERR7803603. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541258 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 8.22694 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 24 Number of CRISPR spacer hits supporting host taxonomy 698 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_1079219__flag_1__multi_6.0000__len_28462_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 71.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8695652173913043 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_1079219__flag_1__multi_6.0000__len_28462_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0272278 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Mushuvirus; Faecalibacterium virus Mushu virus enrichment approach none ERS11143224 SAMEA13541259 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7803603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541259 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 68.6673 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 171 Number of CRISPR spacer hits supporting host taxonomy 138 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_1818991__flag_0__multi_50.9916__len_119818_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6363636363636364 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_1818991__flag_0__multi_50.9916__len_119818_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_provirus.1818991 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143225 SAMEA13541260 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7803603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541260 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 182.827 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 15 Number of CRISPR spacer hits supporting host taxonomy 88 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_24103__flag_0__multi_137.3275__len_25186_1 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 55.38 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8333333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_24103__flag_0__multi_137.3275__len_25186_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738247_virus.1820 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143226 SAMEA13541261 2100421 uncultured Caudovirales phage This sample represents an uncultured Caudovirales provirus assembled from ERR7803603. BACPHLIP temperate score 0.75 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541261 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 84.3587 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 110 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_2832454__flag_0__multi_77.8954__len_59234_1 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 95.92 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.875 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_2832454__flag_0__multi_77.8954__len_59234_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0345548 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales virus enrichment approach none ERS11143227 SAMEA13541262 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7803603. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541262 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 23.6496 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 7 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_3136066__flag_0__multi_18.0000__len_235671_1 Viral contig found in MAG ERR7803603_bin.389 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.11 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.4090909090909091 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_3136066__flag_0__multi_18.0000__len_235671_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME039567 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632;s__CAG-632 sp900539185 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_provirus.3136066 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143228 SAMEA13541263 2100421 uncultured Caudovirales phage This sample represents an uncultured Bacteroides phage F2 provirus assembled from ERR7803603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541263 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 174.589 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_3347351__flag_0__multi_120.9793__len_58066_1 Viral contig found in MAG ERR7803603_bin.457 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 73.81 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_3347351__flag_0__multi_120.9793__len_58066_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME271908 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_provirus.3347351 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2 virus enrichment approach none ERS11143229 SAMEA13541264 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae provirus assembled from ERR7803603. BACPHLIP temperate score 0.0875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541264 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 49.9589 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 296 Number of CRISPR spacer hits supporting host taxonomy 159 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_482770__flag_0__multi_38.9846__len_103861_1 Viral contig found in MAG ERR7803603_bin.340 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type provirus (UpViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_482770__flag_0__multi_38.9846__len_103861_1 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0226686 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143230 SAMEA13541265 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.9375 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541265 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 265.234 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 34 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_103624__flag_3__multi_198.0000__len_38807 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.47368421052631576 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_103624__flag_3__multi_198.0000__len_38807 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738227_bin.197 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella;s__Angelakisella sp004557855 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.103624 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143231 SAMEA13541266 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.975 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541266 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 12.4926 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 8 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_1141585__flag_0__multi_8.9916__len_19174 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 53.17 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9230769230769232 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_1141585__flag_0__multi_8.9916__len_19174 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7746111_bin.94 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__;s__ vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1141585 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143232 SAMEA13541267 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541267 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:08Z INSDC last update 2022-12-27T19:09:08Z INSDC status public MAG coverage depth 254.299 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 9 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_1344811__flag_3__multi_192.0000__len_270575 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 10 number of unique standard tRNAs extracted 9 percent of BLAST hits supporting viral taxonomy 0.4929577464788733 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_1344811__flag_3__multi_192.0000__len_270575 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME000247 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter;s__Intestinibacter bartlettii vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1344811 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143233 SAMEA13541268 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.95 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541268 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:07Z INSDC last update 2022-12-27T19:09:07Z INSDC status public MAG coverage depth 16.042 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 10 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_1536052__flag_1__multi_12.0000__len_38164 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.84375 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_1536052__flag_1__multi_12.0000__len_38164 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1536052 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143234 SAMEA13541269 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 1 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541269 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:07Z INSDC last update 2022-12-27T19:09:07Z INSDC status public MAG coverage depth 18.3138 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 14 Number of CRISPR spacer hits supporting host taxonomy 37 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_1732044__flag_0__multi_13.9968__len_41042 Viral contig found in MAG ERR7803603_bin.452 assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 2 number of unique standard tRNAs extracted 2 percent of BLAST hits supporting viral taxonomy 0.8518518518518519 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_1732044__flag_0__multi_13.9968__len_41042 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME256853 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302;s__CAG-302 sp001916775 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.1732044 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143235 SAMEA13541270 336724 Myoviridae environmental samples This sample represents an uncultured Muvirus virus assembled from ERR7803603. BACPHLIP temperate score 0.13945538818076478 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541270 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 2258.6 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 98 Number of CRISPR spacer hits supporting host taxonomy 99 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_2020044__flag_0__multi_1662.0461__len_36355 Viral contig found in MAG ERR7803603_bin.559 assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; HMM-based (lower-bound) completeness score 54.46 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.9545454545454546 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_2020044__flag_0__multi_1662.0461__len_36355 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7745836_bin.70 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio;s__Succinivibrio sp000431835 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.2020044 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Muvirus virus enrichment approach none ERS11143236 SAMEA13541271 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.05481795254560153 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541271 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 56.8169 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 131 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_2262605__flag_0__multi_38.9811__len_40247 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 83.23 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.75 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_2262605__flag_0__multi_38.9811__len_40247 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME096004 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__Desulfovibrio piger vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745687_virus.1060 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143237 SAMEA13541272 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.0125 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541272 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 172.891 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 29 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_2619768__flag_0__multi_108.3187__len_20057 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.49 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7272727272727273 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_2619768__flag_0__multi_108.3187__len_20057 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_virus.1648 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143238 SAMEA13541273 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541273 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 189.193 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 1 Number of CRISPR spacer hits supporting host taxonomy 7 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_281093__flag_1__multi_141.0000__len_50028 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6521739130434783 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_281093__flag_1__multi_141.0000__len_50028 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7738202_virus.338 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143239 SAMEA13541274 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.05 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541274 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 128.135 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_3005186__flag_1__multi_97.0000__len_272373 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8771929824561403 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_3005186__flag_1__multi_97.0000__len_272373 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7746748_virus.31 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143240 SAMEA13541275 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.12085444902106184 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541275 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 51.2947 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 16 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_311282__flag_0__multi_38.3615__len_30799 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 76.97 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6111111111111112 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_311282__flag_0__multi_38.3615__len_30799 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME176098 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;s__CAG-83 sp000435975 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.311282 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143241 SAMEA13541276 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.1881217983453865 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541276 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 365.535 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 0 Number of CRISPR spacer hits supporting host taxonomy 5 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_3275206__flag_0__multi_269.8721__len_21151 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 54.55 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_3275206__flag_0__multi_269.8721__len_21151 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7745816_virus.1542 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143242 SAMEA13541277 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541277 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 98.4193 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 2 Number of CRISPR spacer hits supporting host taxonomy 136 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_3460096__flag_0__multi_64.8468__len_23944 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 66.65 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6153846153846154 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_3460096__flag_0__multi_64.8468__len_23944 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host ERR7738937_bin.183 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;s__ER4 sp000765235 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.3460096 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143243 SAMEA13541278 336724 Myoviridae environmental samples This sample represents an uncultured Myoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.7 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541278 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 20.5452 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 295 Number of CRISPR spacer hits supporting host taxonomy 205 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_3571498__flag_3__multi_16.0004__len_45109 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.8529411764705882 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_3571498__flag_3__multi_16.0004__len_45109 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;unk;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative MGV-GENOME-0354261 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae virus enrichment approach none ERS11143244 SAMEA13541279 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541279 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:07Z INSDC last update 2022-12-27T19:09:07Z INSDC status public MAG coverage depth 24.9167 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy NA Number of CRISPR spacer hits supporting host taxonomy NA Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_3571527__flag_3__multi_20.0005__len_41556 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.7391304347826086 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_3571527__flag_3__multi_20.0005__len_41556 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host NA vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.3571527 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143245 SAMEA13541280 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541280 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 17.4798 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 13 Number of CRISPR spacer hits supporting host taxonomy 1 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_471886__flag_1__multi_12.9903__len_39802 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (medium-confidence) completeness score 86.61 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted 1 number of unique standard tRNAs extracted 1 percent of BLAST hits supporting viral taxonomy 0.7142857142857143 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_471886__flag_1__multi_12.9903__len_39802 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host GUT_GENOME256714 tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95;s__CAG-95 sp000438155 vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.471886 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143246 SAMEA13541281 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.9875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541281 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T04:22:35Z INSDC last update 2022-12-27T04:22:35Z INSDC status public MAG coverage depth 22.168 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 3 Number of CRISPR spacer hits supporting host taxonomy 736 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_751770__flag_0__multi_17.0000__len_36743 Viral contig found in MAG NA assembly quality Many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; AAI-based (high-confidence) completeness score 62.3 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.5833333333333334 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_751770__flag_0__multi_17.0000__len_36743 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.751770 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none ERS11143247 SAMEA13541282 2133760 Siphoviridae environmental samples This sample represents an uncultured Siphoviridae virus assembled from ERR7803603. BACPHLIP temperate score 0.8875 ENA-FIRST-PUBLIC 2022-12-27 ENA-LAST-UPDATE 2022-12-27 External Id SAMEA13541282 INSDC center alias Stanford University School of Medicine INSDC center name stanford university school of medicine INSDC first public 2022-12-27T19:09:07Z INSDC last update 2022-12-27T19:09:07Z INSDC status public MAG coverage depth 65.7051 MAG coverage software Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15. Number of BLAST hits supporting host taxonomy 23 Number of CRISPR spacer hits supporting host taxonomy 119 Submitter Id Hadza_MoBio_hadza-A-D_C_6_1128__k127_856916__flag_0__multi_47.0000__len_42879 Viral contig found in MAG NA assembly quality Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. assembly software MEGAHIT;1.2.8;--meta-large collection_date 2013-09-07 completeness approach CheckV; DTR (high-confidence) completeness score 100 completeness software CheckV;0.8.1;end-to-end, database v1.0 detection type independent sequence (UViG) environment (biome) terrestrial biome environment (feature) human-associated habitat environment (material) feces feature prediction Prodigal;2.6.3;meta geographic location (country and/or sea) Tanzania geographic location (elevation) 1287 geographic location (latitude) -3.55 geographic location (longitude) -34.58 host prediction approach CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6). investigation type uncultivated viral genomes isolation_source human feces metagenomic source human gut metagenome nucleic acid extraction https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 number of standard tRNAs extracted NA number of unique standard tRNAs extracted NA percent of BLAST hits supporting viral taxonomy 0.6666666666666666 predicted genome structure non-segmented predicted genome type dsDNA project name Human gut UViGs reference database(s) NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022) reference for biomaterial https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample collection device or method https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103 sample derived from ERS2585552 sample name Hadza_MoBio_hadza-A-D_C_6_1128__k127_856916__flag_0__multi_47.0000__len_42879 sequencing method Illumina NovaSeq 6000 similarity search method diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5 source of UViGs metagenome (not viral targeted) species-level group of predicted host NA tRNA extraction software tRNAscan-SE;2.0.9;-B taxonomic classification Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used. taxonomy of predicted host d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83;unk;unk vOTU classification approach 95% ANI;85% AF;greedy, centroid-based vOTU database MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0 vOTU representative ERR7803603_virus.856916 vOTU sequence comparison approach blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90 viral identification software CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults viral taxonomy Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae virus enrichment approach none